John Shepard (MR)

"This war’s brought us pain, suffering, and loss. But it’s also brought us together, as soldiers, allies… friends. This bond that ties us together is something that the Reapers will never understand. It’s more powerful than any weapon, stronger than any ship. It can’t be taken or destroyed. The next few hours will decide the fate of everyone in the galaxy. Every mother. Every son. Every unborn child. They’re trusting you. Depending on you to win them their future. A future free from the threat of the Reapers! But take heart! Look around you! You’re not in this fight alone. We face our enemy together, and together, we will defeat them!"

- Commander John Shepard, rallying his squad

First Minister John Shepard (service no. 5923-AC-2826) is a legendary N7 soldier in the Systems Alliance military, the first human Spectre, and the main protagonist of the Mass Effect trilogy. Born in Vancouver in 2154, he had a difficult childhood but was able to escape the life of petty crime and underworld gangs upon enlisting in the Alliance Navy.

A decorated war hero, Shepard is a veteran of the Skyllian Blitz and served with distinction which earned him the Alliance's highest award, the Star of Terra, for almost single-handedly repelling an assault from batarian slavers on Elysium long enough for reinforcements to arrive. Following the battle, he is arguably considered one of the Alliance's most famous soldiers. By overcoming great challenges in the line of duty, Shepard has since shown exemplary talent and leadership capabilities which led to him to undergo N7 training in Rio de Janeiro. He later served as Executive Officer (XO) of the SSV Normandy SR-1 under the command of Captain David Anderson.

During the Eden Prime War, he helped expose Saren Arterius for his involvement with the geth attack on Eden Prime. He also became friends with Kaidan Alenko, Ashley Williams, Garrus Vakarian, Urdnot Wrex, Tali'Zorah nar Rayya, and Dr. Liara T’Soni, who helped him uncover the existence of a race of ancient sentient machines known as Reapers. For his efforts, Shepard was appointed the first human Spectre and assumed command of the Normandy when Anderson was forced to step down. After witnessing Kaidan’s sacrifice to destroy Saren’s research facility during the mission on Virmire, Shepard continued to help lead the war effort against the geth and foil Saren’s plans. Not long after, Williams, with whom Shepard had fallen in love, encouraged him to remain vigilant. Not long after, Shepard and his crew participated in the Battle of the Citadel. During the campaign, Saren was killed and the Reaper vanguard, Sovereign, was destroyed. Although widely praised for saving the Citadel from a surprise attack, his theories about the Reapers have caused political controversy and despite calls for him to cease his investigation, he continued to work tirelessly in an attempt to try to find a way to stop the new threat. Shortly thereafter, he was killed in action by the Collectors.

Two years later, he was brought back to life under the Lazarus Project by the pro-human syndicate known as Cerberus. With the assistance of the organization’s enigmatic leader, the Illusive Man, Shepard assumed command of the Normandy SR-2 and a crew. With the help of his new teammates Miranda Lawson, Jacob Taylor, Zaeed Massani, Mordin Solus, Grunt, Kasumi Goto, Thane Krios, Jack, Samara and Legion, Shepard set out on a mission to stop the Collectors’ galaxy-wide campaign of human abductions as they worked in conjunction with the Reapers. Over the course of the journey, Shepard participated in the final assault on the Collectors’ main base of operations accessible only through the Omega-4 Relay and managed to destroy their base, thus putting an end to the Collectors once and for all. Soon after the mission was completed, he severed all ties with Cerberus and operated independently over the next year. During this time, he helped Liara defeat the Shadow Broker. Shepard soon fell out of favor with the Alliance when he blew up the Bahak system and killed its 300,000 batarian colonists as collateral damage in an attempt to delay the Reapers from invading. As a consequence, he was relieved of duty and imprisoned at an Alliance military base on Earth to await trial.

Six months later, however, the Reapers returned from dark space and began their next galaxy-wide invasion. Shepard was forced to escape Earth on the Normandy, but not before being re-instated into the Alliance military and being tasked with gathering help from other species to build an ancient superweapon dubbed the "Crucible". During the course, he successfully negotiated an alliance between the turians and krogan upon curing the genophage and ending the three-hundred year conflict between the quarians and geth. Under Hackett and Shepard's leadership, the combined fleets of all the races of the galaxy launch a massive final attack on the Reapers orbiting Earth and on its surface in a last-ditch effort to retake the Citadel and use it to activate the Crucible. Through many hardships and even sacrifices, Shepard used the Crucible to destroy the Reaper threat and put an end to the 50,000-year cycle of extinction.

Due to his injuries and plagued by survivor's guilt, Shepard resigned his commission in the Alliance military and withdrew from the public eye, though he would later contribute to the Citadel Council’s reorganization into the Interstellar Republic and became one of its prominent leading figures. During this time, Shepard and Williams were married and had four children.

By 2196, Shepard was nominated by First Minister Linariley T’eavius, and confirmed by the Senate, to serve as Minister of Defense. During the Great Galactic War, however, Linariley and most of her cabinet were killed when the yahg attacked the Citadel. Being the designated survivor, Shepard succeeded Linariley as First Minister. The following year, Shepard signed into law the Yahg Demilitarization and Confinement that ended the war and presided over another galaxy-wide recovery effort. He retired in January 2208 due to term limits and kept a low profile, but was coaxed out of retirement to assist his son Kaidan in the final battle against the extra-galactic targarium species.

Early life
"The city on Earth where I grew up was hard and dirty. I can see it as a warzone."

- John Shepard, about his childhood

"Shepard was born on Earth and orphaned at an early age. He managed to survive on the streets until he was able to enlist at 18."

- An Alliance military dossier

Born on April 11, 2154 in the city of Vancouver on Earth, John Shepard never knew his parents or any of his family that well, having been abandoned by them not long after his latent biotic abilities manifested, feeling that this was the type of punishment from a universe that obviously hated him and anything about him. When he turned six, Shepard found his freedom with the Tenth Street Reds, beginning a life of gang violence and turf wars. He was initiated into the gang and eventually participated in many gang wars and turf wars between rival factions. Despite trying to keep his distance, a gang member attempted to kill him after the violent battle. Finch and Julius Shaw saved him from his execution, with Finch killing the small-time hoodlum. Julius informs the gang that it is time to take the fight to the three rival gangs: Smoking Barrels, Pura Sapiens, and Venom Kick.

For years he pulled off petty crimes, robberies, even holding people at gunpoint. But it wasn’t until one fateful night that caused Shepard to begin rethinking his decision: a robbery went wrong when he watched as one of his fellow gang members was gunned down by a store owner. When he fled the scene he couldn’t help but think to himself that could’ve been him. Shepard's youth was filled with violence and crime but sought a way to clear himself of his vile past and create a new future for himself, since his life in constant violence threatened to consume him.

Basic training
On his eighteenth birthday, Shepard enlisted in the Alliance Navy and came to celebrate his enrollment more than his birthday. After joining the military, Shepard boarded a shuttle that took him to the Macapá Training Camp in Brazil, one of the largest military training centers. There, he began his basic training under some of the toughest and most experienced combat drill instructors, such as Gunnery Chief Ellison. By the end of his basic training, Shepard graduated top of his class from the Alliance Naval Academy and took several weeks off to relax at a military base on Shanxi before boarding a shuttle for shore leave on Arcturus Station.

The Skyllian Blitz
"He proved himself during the Blitz. Held off enemy forces on the ground long enough for reinforcements to arrive."

- Admiral Steven Hackett

In 2176, a young 22 year-old Shepard was stationed on Elysium during shore leave alongside a few other marines he graduated with. However, later that night, Shepard was woken up by an unexpected attack when the first wave of the Skyllian Blitz struck. A massive coalition of slavers, crime syndicates and batarian warlords, many of which were under the command of Elanos Haliat, led an attack on the colony in an attempt to gain prestige amongst the gangs of Omega. Nearly three hours in the structure, they began to make their escape, only to find the entire hotel was crumbling. Surviving the building’s collapse, Shepard and other marines he had rounded up to initiate a counterattack against the overwhelming pirate forces.

From courtyards to skyscrapers, Shepard became well-known among the citizenry, marines, and most importantly, the attacking mercenaries. Eventually, Shepard’s attacks caught up with him and found himself, several marines and local militia surrounded by enemy forces. Shepard ordered the survivors to evacuate the civilians while preparing for the approaching 10,000 batarians, who easily outgunned and outnumbered him. Using the last supplies of ammunition and grenades, he laid waste to a large number of the enemy forces, but eventually found his weapons empty. In a last ditch effort, Shepard engaged in hand-to-hand combat to ravage the remaining forces, until eventually the building collapsed; his demise was greatly expected. Astoundingly, he succeeded in eliminating the first wave of enemy troopers before reinforcements arrived.

Haliat's plans came to nothing as the Alliance repelled the Blitz and decimated the pirate ships from orbit. The Terminus pirates blamed Haliat for the Blitz's failure, and he lost his position as their leader. He then retreated to a remote world in disgrace. News later reached Shepard that the soldiers under his command and the colonists made it out alive. Meanwhile, Shepard was recognized amongst the Alliance and galactic society, with a bright future. He received several accommodations, medals, and awards (including the Star of Terra) for his participation in the battle. The following year, he was accepted into Officer Candidate School and promoted, although he was already recognized as one of the best soldiers in the Alliance military.

N7 commendation
Because of his actions during the Skyllian Blitz, Shepard was recommended by the Alliance brass to undergo N7 training at the Interplanetary Combatives Academy in Rio de Janeiro. The aspiring lieutenant received the "N" military vocational code rating, being one of 300 out of 750 to graduate.

Shakedown run
In the year 2183, with numerous achievements under his belt, Shepard was named Executive Officer (XO) of the SSV Normandy SR-1, an advanced prototype Alliance stealth frigate, under the command of his close personal friend and mentor Captain David Anderson. On board, Captain Anderson is in discussion with Admiral Steven Hackett and Ambassador Donnel Udina concerning Commander Shepard’s worthiness to become the first human Spectre, an elite agent for the Citadel Council. Meanwhile, the ship and crew are heading to Eden Prime in the Utopia system for their shakedown mission. Everything began to move in a positive direction.

However, everything changed when they intended to make a covert pick up on the human colony of Eden Prime. Shepard heads to the bridge where Joker, the pilot, guides the ship into the mass relay. Because of the presence of Nihlus Kryik, a turian Spectre sent by the Council to observe, and the famed Captain Anderson, several members of the crew think their true purpose at Eden Prime is far more important than a simple shakedown run. After making the jump, Captain Anderson asks Shepard to come to the comm room for a briefing.

Nihlus has time to speak to Shepard before Anderson joins them. Together they inform the commander that a Prothean beacon has been discovered on Eden Prime. Prothean technology has immense scientific value, but since Eden Prime is close to the Terminus Systems, the beacon is at risk from pirates and mercenary bands. This is the Normandy ' s true objective: recover the beacon. This mission will also be Nihlus' chance to observe Shepard in action, the first of several they will undertake together to assess Shepard's candidacy for the Spectres.

The briefing is interrupted by a transmission from Eden Prime that Joker patches through. The footage shows Alliance soldiers fighting on the surface, under heavy fire and requesting reinforcements. As Shepard, Anderson and Nihlus watch, they see a huge dreadnought hanging over the surface. Anderson orders Shepard to get ready—this is going to be worse than they thought.

Attack on Eden Prime
"I know Saren. I know his reputation, his politics. He believes humans are a blight on the galaxy. This attack was an act of war. He has the secrets from the beacon. He has an army of geth at his command. And he won’t stop until he’s wiped humanity from the face of the galaxy."

- Captain David Anderson to Commander Shepard

As the Normandy touches down on Eden Prime, Corporal Richard Jenkins, Staff Lieutenant Kaidan Alenko and Commander Shepard prepare to head down to the planet. Nihlus is going groundside too, but goes on ahead. In the first few minutes on the surface, geth assault drones appear without warning and cut down Jenkins. Shepard and Alenko continue towards the dig site, discovering one of the few surviving marines, Gunnery Chief Ashley Williams, who is being chased by geth troopers. Shepard and Alenko help her fight them off. Williams can't explain why the geth are here, but they've wiped out her whole unit.

Williams leads them to the dig site but the beacon has been moved to the spaceport. While they examine the nearby camp, the squad ran into a group of Husks, human corpses reanimated by the geth, which they kill. Shaken, they continue towards the spaceport where Nihlus agreed to meet with them. Unfortunately, by the time they arrived he was found dead.

After finding Nihlus's body, Shepard's team continues to the tram area where they defeat the last of the geth and disarm their demolition charges. Shepard sees the beacon and calls the Normandy while Alenko and Williams take a look at it. One of them gets too close and is caught in some sort of field—Shepard intervenes and throws Williams out of the way but is caught in the field instead, pulled off the ground as Saren was. The commander suffered a horrific vision: synthetics waging a terrible war before the beacon exploded and Shepard was thrown to the ground, unconscious.

First human Spectre
"The mission to Eden Prime was top secret. The only way you could’ve known about it was if you were there."

- Commander Shepard to Saren Arterius

Fifteen hours after the Eden Prime attack, Shepard wakes up in the Normandy ' s medical unit, much to the relief of Alenko and Williams. Dr. Karin Chakwas says the commander is physically okay, but has increased rapid eye movement and unusual beta waves, indicating psychological trauma. Shepard mentions the vision but can't explain it. Captain Anderson briefs Shepard about Saren. He is a powerful and legendary Spectre but also outspoken against humans. If Saren is in charge of the geth, that means he has gone rogue, and they must tell the Council. Upon arriving at the Citadel, Ambassador Udina tries to convince the Council to remove Saren's rights and privileges as a Spectre, but only succeeds in getting an audience. Shepard, along with Alenko and Williams, continues to the Citadel Tower and meets Garrus Vakarian, a turian C-Sec officer investigating the charges against Saren. He hasn't found anything useful: Saren's Spectre status makes him untouchable.

The Council audience doesn't go well. The Alliance has little evidence and Saren—viewing the proceedings from a hologram—openly laughs at Shepard's vision. They need more to go on. Garrus, the C-Sec officer, might be able to help. Udina tells Shepard to find Harkin, a suspended C-Sec officer who could help them find Garrus. Anderson also suggests speaking to Barla Von, a financial expert on the Citadel who works for the Shadow Broker. When Shepard heard Garrus was last seen in the Med Clinic, the commander intercepts a couple of thugs threatening Dr. Chloe Michel, and saves her with Garrus' help. From the two of them, Shepard learns that a quarian has recently arrived on the Citadel, claiming to have evidence of Saren's connection to the geth. However this quarian is being held captive by Fist, a local crime lord who used to work for the Shadow Broker, but who's now betrayed the Broker to work for Saren.

Along with Garrus, the group gains the aid of Urdnot Wrex, a krogan battlemaster, mercenary and bounty hunter who has been sent by the Shadow Broker to kill Fist. They raid Chora's Den and discover the quarian was supposed to hand the information over to the Shadow Broker, but this meeting is a trap. Saren's men will be the ones waiting. Shepard races to the meeting and manages to save the quarian, Tali'Zorah nar Rayya. They bring Tali back to the Ambassador's office.

The evidence she found was an audio file she managed to save from a geth memory core, which has clear evidence Saren was behind the attack on Eden Prime. However, the file also hints that Saren is looking for something called the Conduit with the aid of a powerful asari called Matriarch Benezia, to bring about the "return of the Reapers". When the evidence is presented to the Council, Saren’s Spectre status was revoked, but they're reluctant to send a fleet after him to apprehend him. No interest is shown in the Reapers.

As people in the Chambers watch in amazement, Commander Shepard becomes the first human Spectre and is tasked with hunting Saren down. Captain Anderson steps down as commander of the Normandy and hands the ship over to Shepard, along with some useful leads. There have been reports of geth activity on the planets Noveria and Feros. Also, Matriarch Benezia, Saren's ally, has a daughter named Dr. Liara T'Soni, a Prothean expert who may have useful information. Shepard was furious, feeling that Anderson was being forced out of office but eventually came to accept the sacrifice. After giving the crew a speech, Shepard is now in command of the Normandy.

Search for Dr. Liara T'Soni
"Anderson decided to stay behind, giving up his ship, the Normandy. He told me I would need it more than he would. He also pointed me in a direction: Liara, a Prothean expert, adept in biotics and maybe most importantly, daughter of Benezia, Saren’s top lieutenant. And like most asari, as beautiful as she is intelligent and born with a unique ability to meld with other species. Liara was able to help me decipher some of the vision the beacon had given me. Nothing concrete, but it gave me some clues… and a new appreciation for the asari. Her technique for accessing my vision was unexpected, but not at all unpleasant."

- Shepard's journal entry

The Normandy tracks Dr. Liara T'Soni to Therum, a mining colony in the Knossos system of the Artemis Tau cluster, but the geth are already on the surface, taking over several refinery facilities and dropping Geth Armatures from overhead.

Shepard led the squad to a mineshaft and down into a Prothean ruin, where they find Liara trapped behind a Prothean barrier curtain, who explains that she tried to protect herself from the geth but must have pressed something she wasn’t supposed to and pleads for assistance to get out. Freeing her with a mining laser, they discover she is not in league with Saren and has no idea what the Conduit might be. Liara also warned them that there are more geth being led by a krogan. Then a tremor is felt in the mine. The ruins were not entirely stable and the mining laser must have triggered a seismic event, prompting Shepard to tell Joker to get the Normandy over the ruins as quickly as he can make it. As the squad leaves the ruined tower with Liara, they are confronted by a krogan battlemaster who is leading the geth and manage to defeat him as the unstable ruins begin to collapse. They escape just in time.

Joker welcomes Shepard and the squad back to the Normandy with more than a bit of sarcasm. During the debriefing, Liara explains her expertise is on the Prothean extinction. She has a theory they were not the first civilization to mysteriously vanish, and is amazed by Shepard's story of the Reapers and offers to link her mind with Shepard’s to try to make sense of the vision from Eden Prime. The joining doesn’t produce any results and Liara gets tired. Shepard dismisses the crew and reports his mission to the Council.

Noveria
"Thanks to Liara’s help, we had our next lead: Benezia. Saren had taken her to Noveria where he enslaved a dangerous race of insect-like creatures: the rachni. He ordered Benezia to use the same technique Liara had used on me to extract information from the Rachni Queen. The queen’s drones were everywhere, and they weren’t happy. We had to fight through hundreds of them to get to Benezia. By the time we arrived, Saren was gone… with the information."

- Shepard's journal entry

Next, Shepard and his team headed to Noveria, hoping to find Matriarch Benezia herself. Noveria's capital of Port Hanshan did not treat him well upon arrival. Not only were they hesitant to let in an armed Spectre squad, but they wouldn't let him leave to investigate. Eventually Shepard had earned a few favors, collecting enough incriminating evidence that Administrator Bel Anoleis was corrupt to get him a garage pass. This allowed him to leave, but was ambushed by geth. After a brief firefight and a warning to Port Hanshan Security, Shepard's squad set off.

The facility is deserted save for geth and bizarre creatures: the rachni, which have escaped from the labs. Shepard reactivates the Peak 15 station’s virtual intelligence, Mira, and goes up to Rift Station looking for Benezia. Rift Station is full of science staff sheltering from the rachni attack; Shepard helps them out but gets attacked by those loyal to Benezia. The squad finds out Binary Helix discovered a rachni egg that turned out to be a queen, and were trying to breed an army from her brood until the rachni turned on them.

Down in the labs through the maintenance area, Shepard finds Benezia with the Rachni Queen. The matriarch attacks the squad, but after a fierce battle Benezia manages to overcome the indoctrination that Saren has used to control her, and tells Shepard the truth. Saren wants the location of the lost Mu Relay, and sent her to retrieve it from the queen's genetic memory. Benezia doesn't know what else he is planning. She hands the coordinates over to Shepard, but becomes lost to the indoctrination again and the commander has to kill her. Before they had the chance to leave though they were confronted by a corpse, it was under the control of the Rachni Queen. She questioned whether she would be killed or set loose; eventually Shepard made his decision and freed the queen, giving the rachni another chance, much to Wrex’s chagrin. Their next step was to clear the facility of rachni and escape, and with some help they managed to succeed with help of the Neutron Purge, though they barely escaped in time.

Asteroid X57 hostage crisis
"Listen – we don’t have much time. The batarians fired up the fusion torches. You’ve got to shut them down before we hit Terra Nova!"

- Simon Atwell to Commander Shepard

At some point, a batarian extremist group hijacked a mobile asteroid station Asteroid X57 in the Asgard system and set it on a collision course with the nearby human colony of Terra Nova. The Normandy’s computer alerts Shepard and the hand-picked crew that X57 is heading to Terra Nova too fast, and is on course to hit the planet within four hours. The crew then quickly rushes in to try to save the millions of innocent civilians before the asteroid completes its deadly descent.

Inside, Shepard and the squad encounter five batarian troopers, a batarian sniper, and a pack of four varren. The first two varren are dropped in a matter of minutes, with a second pair of war beasts released shortly after that – when a batarian shouted "Release the varren!" Once the batarians were cleared out, the group shuts down the fusion torch station and is again contacted by the unknown woman, Kate Bowman. She says batarian extremists have attacked the asteroid and doesn’t know why the batarians are here, but they’ve killed many of the personnel on the asteroid. However, she signs off before she’s discovered. As Shepard leaves the fusion torch station, he’s shot by a nervous Simon Atwell; however, his shields deflect the shot. Simon gives Shepard as much information about the asteroid, Kate, and the batarian attack. Simon reveals that the asteroid is going to crash into Terra Nova and cause catastrophic damage – not only will it destroy the colony and kill everyone on the surface, but the devastation will effectively kill the planet. When implied about why the batarians are doing this, Simon responds that they’re pirates and slavers, not planet killers, and doesn’t know why they changed from just a slave grabbing run to killing the planet, but he has a warning: the next torch station is surrounded by live blasting caps and that three of his engineers are missing. Simon also says that the batarian leader is named Balak, but doesn’t understand why the batarians are doing this.

Disabling the second fusion torch, Shepard gets another message over the radio from Kate Bowman, saying that the batarians know someone’s shutting down the torches and, to make things worse, intend to blow up the main facility. Before she can finish, the batarian leader Balak pulls her away.

When the third and final fusion torch is shut down, Shepard encounters Charn, Balak’s second-in-command, who tries to negotiate, claiming that he and his men had only signed on for a simple slave grab, not to destroy a colony. He is under orders to kill Shepard but he’s getting tired of following Balak’s little crusade. Shepard convinces Charn to leave the asteroid peacefully, under the promise that Balak will be eliminated and Charn will then be the one calling the shots. In that event, Charn agrees immediately and provides Shepard with a pass to the main facility along with a warning that Balak is a "mean bastard".

When the Commander launches an assault on the main facility, Shepard confronts Balak, who has planted a bomb in the offices where the hostages are being held. He is furious that the torches have been shut down and sees this as an act of reprisal for the early stages of humanity’s major expansion in the Skyllian Verge, claiming territories and resources he believes should have belong to the batarians, all because the Council saw a military advantage in befriending the Alliance. Balak talks angrily about the thwarted Skyllian Blitz and holds Shepard personally responsible for the Blitz’s failure and accuses him of murdering batarians on Torfan, saying what he’s doing is no different. Shepard rebuffs this notion, retorting that the batarians attacked first and when the Alliance retaliated, the batarians "ran like cowards". Out of patience, Balak reveals that the hostages are locked away in a room with an explosive that he’s prepared to detonate, unless the Commander offers him safe passage out of the building and off the asteroid.

Faced with a choice of letting Balak and risk him causing havoc in the future but save the hostages or attack him knowing the hostages will be sacrificed, Shepard begrudgingly let Balak go to save the hostages, though he warned the batarian that the next time he causes trouble he’ll be ready for him. Disarming the three explosive charges around the room while under fire, the hostages were spared. Once freed from one of the offices, Shepard finally meets Kate Bowman, who is glad to be alive but devastated at the death of her brother and colleagues. Kate realizes she never even asked the Commander’s name, and claims Shepard isn’t what she expected, but she’s very grateful for the help.

After the battle, Shepard meets Simon Atwell again, who is saddened by Balak’s escape. He confirms that Shepard’s efforts were not in vain: the asteroid was on a direct course for Terra Nova’s capital, and now that the torches have been disabled, X57 will miss the planet safely.

Feros
Drawn to Feros by rogue geth activity, Shepard and the squad arrive at the colony of Zhu's Hope, owned by ExoGeni Corporation. The colony has been suffering repeated geth attacks and the settlers there are acting strangely. Shepard clears the geth for the colonists and takes a Mako along the Prothean Skyway to the main geth base. The squad finds a small group of colonists who have become separated from the others, led by Juliana Baynham and a nervous ExoGeni representative, Ethan Jeong. Despite their situation these survivors seem to be coping better than Zhu's Hope. Before they leave, Juliana asks Shepard to look for her daughter Lizbeth, whom she believes to be still inside ExoGeni Headquarters.

After making their way inside the ExoGeni Headquarters, Shepard's squad finds Lizbeth, scared but alive. From the company VI, Shepard discovers that the corporation has been experimenting with a mind-controlling plant, the Thorian, and that Zhu's Hope is actually a testing ground for ExoGeni to study its abilities. Shepard disables the force fields that the geth have set up by knocking the geth dropship off the headquarters and returns to the Skyway group. Jeong has received word that ExoGeni wants Zhu's Hope purged. Shepard deals with Jeong and heads back to Zhu's Hope to find the Thorian.

Controlled by the Thorian, the colonists attack Shepard on sight. Some have been turned into Thorian Creepers. Shepard can use special gas grenades that instantly kill the creepers and harmlessly paralyzes the colonists, then descends beneath Zhu's Hope to find the Thorian. It is an enormous creature that looks nothing like a plant. It creates an asari clone to speak for it, but only to tell Shepard it's not interested in bargaining with "meat". After battling waves of Thorian Creepers and clones, Shepard manages to destroy the Thorian's neural nodes and it falls to its death.

An asari emerges from a Thorian pod, and manages to explain what happened. Shepard learns that Saren sacrificed his asari ally, Shiala, to the Thorian to gain the Cipher. This is the cultural and ancestral experience of the Protheans, which is necessary to understand the vision that the Eden Prime beacon put in time to adjust, the vision will make more sense and hopefully lead them to the Conduit before Saren.

Virmire
"With Saren’s top lieutenant dead, he was quickly running out of time and places to hide. I tracked him down at his base on Virmire, but we soon learned that it was more than just a base of operations. It was a breeding ground. Saren was breeding an army of krogan. He found a cure for the genophage, a disease inflicted on the krogan to prevent them from breeding and taking over the galaxy. But the krogan Saren was breeding were slaves, mindless beasts that obeyed Saren’s will. I had to destroy the base, and all its research."

- Shepard's journal entry

With Feros and Noveria out of the way, Shepard is contacted by the Council with a possible lead: a salarian Special Tasks Group espionage team on Virmire, investigating reports of Saren's activities, has sent a mission-critical transmission that was almost lost in static. Shepard heads to Virmire and meets the leader of the salarians, Captain Kirrahe. They have found a breeding facility for krogan that Saren is using to create an army.

Kirrahe, realizing he's not getting the reinforcements he needs, asks for Shepard's help destroying it and they develop a plan: while the salarians distract Saren's geth, Shepard will take a team around the back and plant a nuclear device that will wipe out the facility. Conflict arose when Urdnot Wrex pressed to know how Saren was breeding an army, and came close to turning traitor when everyone agreed that the base must be destroyed. Kirrahe asks Shepard for a squad member to help him coordinate the attack—to which Ashley volunteers to help the salarians, but must also deal with Wrex, who is furious that Shepard is willing to destroy a cure for the genophage, a salarian bio-weapon which makes krogan breeding next to impossible. Using his calming tone Shepard managed to talk down the infuriated krogan, assuring him that he did not want to destroy the cure either, but cured krogan under Saren’s command are still slaves but only of a different disease. When Wrex finally calmed down and agreed to help Shepard everyone was in awe, nobody expected he could talk down a krogan.

As Shepard's "Shadow" team worked their way into Saren's base they took down numerous support structures, relieving pressure for the STG squads. When they eventually got inside they were shocked at what they found, everywhere they looked was indoctrinated salarians and prison cells. After a while of exploration Shepard had found another Prothean beacon buried in the facility. After the use of the beacon everything began to make sense to Shepard, the meaning of the visions and even some aspects of Saren's plan and they are confronted by a hologram of Sovereign itself, which is not a Reaper ship but an actual Reaper. After a brief back and forth of threats, Shepard realized the true danger that the galaxy was in: Saren wasn't the real threat, it was the Reapers and Sovereign was the first of many. They began to pick up the pace considerably, Joker had contacted them saying that Sovereign was heading back to Virmire.

Shepard manages to get the nuke set up across the facility only to get a call that the salarians are being attacked and are taking heavy losses. The commander takes a group to help them but as they leave, the geth start attacking the nuke site and Shepard was put in a conflict: both Kaidan and Ashley are in trouble and there's no time to save both. Halfway there Shepard had to make a difficult decision, Williams and the STG team was getting demolished by geth, but the geth were now also assaulting the bomb site. After having to listen to a drawn out fight over the comms between Williams and Alenko, Shepard had to choose and he could only save one. Knowing that Alenko was the only survivor by the bomb site, and that he would die to see the bomb detonate, Shepard headed towards Williams, hoping he still had time to save her and the salarian team. Shepard brings reinforcements, only to be confronted by Saren. He tries to make the commander join his cause but Shepard refuses and fights Saren off. Saren gets away and the team board the Normandy, escaping Virmire as the nuke destroys the facility, leaving Kaidan behind to die in the explosion.

Stealing the Normandy
"I know we’ll all be court-martialed if this doesn’t work out. But part of me loves this!"

- Navigator Charles Pressly

Shepard took his time to grieve for the loss of his friend, and thanks to the undamaged beacon on Virmire, his Prothean vision is now complete. During the debriefing, Liara touches Shepard's mind to interpret it fully. The vision was a distress call intended to warn the Protheans about the Reapers. Liara realizes that the landmarks in the vision are on Ilos, a planet she has studied as part of her Prothean research. Ilos had been impossible to reach because it was only accessible through the Mu Relay, which is why Saren needed the Relay's location from Noveria. After the debriefing, Joker passed on a message for Shepard from the Council: they're putting together a massive multi-species effort to face Saren.

Thrilled that the Council was finally taking this seriously, Shepard returns to the Citadel, wanting to personally lead the assault. But once back at the station, he discovers the Council was only putting up a blockade around the mass relays to stop Saren from reaching the Citadel. Neither they nor Ambassador Udina believe his story about the Reapers and they refuse to send a fleet to Ilos. The Mu Relay is in the Terminus Systems and a Citadel fleet there could start a war. Shepard knows the Normandy ' s stealth systems can get them there discreetly, but the Council was getting tired of Shepard's insistence that the Reapers are the real threat. Udina, wanting to make nice with the Council, grounds the Normandy and locks out the ship's systems and closes all official diplomatic channels.

Frustrated, knowing Saren is close to finding the Conduit and they're losing time, Shepard is grateful when Ashley offers support. A real breakthrough comes when Captain Anderson gets in touch, asking Shepard for a discreet meeting at Flux. Anderson believes the commander's story and knows the Normandy is the only ship that can get Shepard to Ilos. He is going to unlock the Normandy’ systems, allowing Shepard to steal the ship and take her to Ilos. Shepard is concerned that Anderson will be arrested and charged with treason—or worse—but Anderson sees his future as a small price to pay for stopping genocide on a galactic scale.

Shepard goes to the Normandy and waits with Joker on the bridge. With Anderson's help the Normandy ' s systems are unlocked and they escape the Citadel, heading to Ilos. While en route to their destination, Ashley comes to visit Shepard’s quarters, saying that, after a long career of being sidelined by the Alliance, Shepard helps her to feel "good enough", and the two spend the night together. Joker then announces that they're about to pass through the Mu Relay, and they will soon arrive at Ilos. Ashley continues to tease Shepard; she claims to have something important to tell him, but if he wants to hear it, he’ll have to survive the mission and come back to her first.

Ilos
"With my team mostly intact, we chased Saren and his army to Ilos, a long lost planet that had once belonged to the Protheans. As we prepared for what we knew would be a desperate fight, I spoke to my crew. We were just one ship against Saren’s growing army. I assured them all that despite the odds, we could defeat him. […] We arrived on Ilos close behind Saren. Once on the planet, we discovered a Prothean databank that helped me put the final pieces of my vision together. The Reapers had come 50,000 years ago and every 50,000 years before that. Each time purging the galaxy of life. The Protheans had fought and died, like every species before them. But a few survived long enough to leave a parting gift: The Protheans had discovered that the Citadel was the key to controlling the mass relays. By sabotaging the Citadel, they found a way to close the relays to dark space, slowing the Reapers’ return, giving us the time we needed to find a solution to stop the Reapers once and for all. Saren knew this. He was leading his army to take control of the Citadel and reestablish the relays to dark space, bringing the waiting Reapers here to destroy us all."

- Shepard's journal entry

Shepard sees that Saren has already arrived with a fleet of geth dropships, though the Normandy ' s stealth system is keeping them safe for now. Executive Officer Charles Pressly picks up some readings on the planet confirming Saren's presence. However, they could not find a landing zone. Shepard suggests dropping the Mako but they need about 100 meters of open terrain for a safe drop and Pressly can only find at most 20 meters. Joker insists that he can do it. The Mako is successfully dropped outside an ancient bunker, but Saren and his geth have already made it inside, shutting a heavy security door behind them.

Shepard looks for ways to get to the other side of the bunker doors. After fighting through the geth left on guard, Shepard and the squad find a security station and reopen the bunker doors. While in the control room, Shepard discovers an ancient Prothean recording which is heavily damaged. The Cipher allows Shepard to make out some of the words—it's another warning about the Reapers but it's just too broken up. They return to the Mako and enter the bunker.

After driving past cryogenic stasis pods, all apparently shut down, Shepard sees a mysterious energy barrier. As the Mako reaches the barrier, another barrier appears behind them, trapping the squad inside. The only way out is through a door at the side of the wall. After heading down an elevator, Shepard finds an ancient Prothean VI named Vigil, who has information Shepard needs to stop the Reapers.

Vigil unveils a startling revelation. The Citadel is actually a trap; a huge mass relay linking to dark space, outside of the galaxy, where the Reapers are waiting. The keepers are presumed to be one of the earliest races to be indoctrinated by the Reapers, who set them the task of maintaining the Citadel and activating the Citadel Relay when Sovereign signals them. It is also revealed that Sovereign is the vanguard of the Reapers. After every Reaper attack, they leave behind one of their kind to act as a vanguard and to monitor the development of the galaxy's races. Once the galaxy's races are sufficiently advanced, the vanguard will activate the Citadel Relay and usher in the next genocide. The reason the Reapers harvest the galaxy of all advance organic life approximately every 50,000 years is currently unknown. According to Vigil, not even the Prothean scientists could comprehend why they do it. They may be driven by goals that organics find impossible to understand. Once the galaxy is harvested, the Reapers return to dark space to hibernate and conserve energy. In this state, they are apparently vulnerable, so they always seal the Citadel Relay behind them.

When the Reapers last attacked about 50,000 years ago, their genocide of the Protheans lasted for centuries. Ilos' personnel hid in cryogenic stasis, watched over by Vigil. However, as his energy reserves ran low, he followed a contingency plan by shutting off pods of non-essential personnel to conserve energy, hoping that when the time was right, he could safely open the pods. In the end, Vigil managed to save a dozen scientists. The few remaining Protheans on Ilos traveled to the Citadel through the Conduit—a small prototype mass relay, built by the Protheans, enabling a one-way link from Ilos to the Relay Monument in the Citadel Presidium. The survivors altered the signal that the keepers respond to and prevented them from activating the relay to dark space. Vigil also explains that if Sovereign assaults the Citadel alone, the combined power of the Citadel Fleet would be enough to defeat the single Reaper. However, if Sovereign is able to direct an agent to go through the Conduit as a back door and transfer control of the Citadel back to Sovereign, it will be able to manually activate the Citadel Relay and bring in the rest of the Reapers. Sovereign had possibly planned this for centuries after discovering the Protheans' sabotage plan. Vigil gives Shepard a data file that will give the commander temporary control of the Citadel to stop Sovereign. After leaving Vigil, Shepard heads through the archives, down into an old aqueduct guarded by geth, and reaches the Conduit. Saren had already gone through, leaving geth to stay guard.

Meanwhile, Sovereign begun its assault on the Citadel, escorted by a large geth fleet. The commander of the Destiny Ascension, Matriarch Lidanya, attempts to close the Citadel but the station doesn’t respond—the operators at Citadel Control are dead. Saren has begun his attack from within.

Back on Ilos, Shepard sees the Conduit is closing fast. Rushing to the Conduit, the squad evades the geth in the process and drives the Mako through, just before the relay closes. On the now-burning and heavily damaged Presidium, two geth troopers notice a blue glow around the Relay Monument. When they go to take a look, the Mako suddenly bursts through and crushes them, before rolling over and crashing against a wall. The race to stop Saren was on.

Battle of the Citadel
"I think we both expected it would end like this. You’ve lost. You know that, don’t you? In a few minutes, Sovereign will have full control of all the Citadel’s systems. The relay will open. The Reapers will return."

- Saren Arterius to Commander Shepard

Shepard and the team manage to get out of the overturned Mako and use the nearby malfunctioning Avina terminal to get a sit rep. Saren is heading toward the Council Chambers and the whole station is infested with geth. The squad tries taking the elevator to the Citadel Tower, but it stops halfway when Saren locks down the station's systems. Shepard tells the team to suit up and blows out the elevator's glass with a single shot. They have to walk the rest of the way in zero gravity with their boots magnetized.

Meanwhile up in the Chambers, Saren—angrily shooting keepers as he goes—reaches the central console and uses it to take control of the Citadel. As Sovereign gets closer, crushing the Citadel Fleet ships in its path, Saren closes the Wards, creating an impenetrable shell around the Reaper and the Geth Dropships already inside. Sovereign settles on top of the Citadel Tower, preparing to open the Citadel Relay once Saren transfers full control.

Elsewhere Shepard and the team are fighting for their lives against the geth and Saren’s krogan warriors out on the Citadel's exhaust plains, trying to get to the Chambers. A geth dropship appears and starts unleashing shock troopers on them; Shepard activates the Citadel's defense turrets, and with their cover fire, takes the dropship out. Further along they run into several powerful geth turrets and have to use cover to get close enough to destroy them, or manage to sneak down a side route where Krogan Battlemasters are waiting. Eventually they reach a maintenance hatch that leads down into the Council Chambers, now burning and full of Saren's geth. The stairways provide some cover as the team fights towards the central console.

At that moment Saren appears and throws a grenade. Shepard's team is blown aside while the commander takes cover close to Saren. He urges Shepard not to be a fool—everything is lost if Shepard continues resisting Sovereign. Saren boasts that his faith faltered but Sovereign has implanted him, made him partly synthetic, perfect. This is the future of organic life. Shepard couldn’t believe Saren allowed Sovereign to implant him. Shepard tries talking Saren down—and the more Shepard spoke, the more Saren is convinced, but his Reaper implants cause the turian intense pain when he begins to agree with Shepard. With enough convincing, Saren thanks the commander for freeing him before shooting himself in the head, falling to the bottom of the Chambers, through the glass floor and is impaled by a large shard.

Using the central console, Shepard uploads Vigil's program and gains control of the Citadel. With advice from the team, Shepard opens a communication channel and gets Joker, who has the Fifth Fleet just waiting for the commander's word once the mass relays are unlocked. Shepard orders the Fifth Fleet to defend the Destiny Ascension and save the Council. After the orders were given, Joker brings the fleet through the nearby mass relay as Shepard opens the Citadel's ward arms.

As the Fleet engages the ships outside—geth dropships and Sovereign itself—Shepard tells the squad to check Saren and make sure he's dead. They drop down to the bottom of the Chambers—one coldly shoots Saren in the head, while the other confirms the kill to Shepard. Suddenly Saren's body begins to twitch as his implants fire up, burning his flesh away until he is a cybernetic construct like a husk, completely possessed by Sovereign. The shockwaves from his transformation cause the platform to collapse and Shepard falls into the bottom of the Chambers. The squad fights back against the creature, but it is fast and deadly.

Outside, the Normandy leads the attack against Sovereign. The Reaper unleashes a terrible weapon that burns through several Alliance ships, but the Fifth Fleet slowly begins to gain the upper hand. As the squad finally destroyed the cybernetic creature and it burns away to ashes, Sovereign begins to weaken under the Alliance attack and releases its grip on the station. A blast from the Normandy is the coup de grace and the Reaper is destroyed.

In the Chambers, Shepard looks up to see a huge piece of debris from the Reaper heading straight for the Tower. The commander yells for the squad to take cover, just as it hits.

Much later, rescuers enter the Tower looking for survivors. Under a pile of rubble they discover Shepard's team... two of them, badly wounded but alive. Leading the rescuers, Captain Anderson helps them out, assures them that it's all right, and asks where Commander Shepard is. One of the squad looks sadly across the Chambers, where the Reaper debris has crashed into the floor. It would have crushed anyone standing under it. The rescue team helps the squad out of the Chambers, reluctantly believing Shepard died in the crash. Anderson looks back—to see someone moving. Commander Shepard, with a broken arm, managed to climb out from behind the debris and limp towards them, smiling.

Aftermath
"While humanity’s efforts in the war earned us our first seat on the Council, it was a hollow victory. The Reapers were still out there. I knew the fight was far from over, but… as the one who led the fight against Saren, I was given new responsibilities. The choice of humanity’s first councilor was left for me to decide. On the one hand: Udina, the lifetime politician. Ruthless and ambitious, he would easily navigate the political landmines that would soon be put in front of him. The other choice: Captain Anderson, the career soldier. Tough, but fair – but a friend, and someone I could trust. Both great leaders in their own right. Anderson didn’t want the job, which was a sure sign he’d be perfect for it. No ambition to get in the way. The war was over, the threat had passed. In time, the Council would rebuild itself. The Citadel could be repaired. Even the pain of lost friends would fade. But none of that mattered if the Reapers were still out there. And if they were all as powerful as Sovereign, we’d have to find a way to stop them. I had to find a way. I gathered my crew, took my ship, and went in search of answers. Officially the Council would only say I was assigned to cleanup duty, rooting out of any remnants of Saren’s army. Just another routine mission."

- Shepard's journal entry

In gratitude for the sacrifices of the Alliance Fleet and Shepard's help, the Council states that humanity has proved themselves worthy and grants them a Council seat. Shepard personally chose Captain Anderson to represent humanity on the Council, citing the need for leaders with the courage to stand up for what they believe in. When approached by Ambassador Udina, Shepard remarks that he thought the Citadel already had too many politicians and expressed his belief that Anderson would be perfect for the job, because he didn’t want it. The victory and celebration was short-lived, however, as Shepard left the Citadel aboard the Normandy, intending to find a way to stop the Reaper invasion.

Death
"Commander! SHEPARD!!"

- Joker, witnessing to John's sacrifice

Unfortunately, only one month after the Battle of the Citadel, the Alliance sends Shepard to locate and destroy any remaining geth. While on patrol in the Amada system, the Normandy was sent into a sector where three ships were reported to have gone missing in the space of one month.

After four days of fruitlessly searching for signs of geth activity, the Normandy is attacked by an unknown assailant. The ship suffers extensive damage, forcing the crew to evacuate via escape pods. Joker, the helmsman, refused the initial evacuation order believing he could still save the ship and continues to pilot despite the received damage to it and is rescued by Commander Shepard, who drags Joker out of his seat and into an escape pod. Before the commander can board the escape pod himself, however, the Normandy is attacked once again and a blast separated them just as Shepard managed to get Joker inside and is sent flying amidst a series of explosions, barely surviving the Normandy ' s destruction. However, the suit's pressure seals were compromised, sliced by debris and air vents out. Shepard asphyxiates and dies; the Commander’s body is seen entering the atmosphere of a nearby planet below.

The news spread quickly and many people were saddened at the death of the first human Spectre. However, Shepard would not stay dead for long.

Resurrection
Two years later, in an effort undertaken by Cerberus, Shepard was brought back to life and awakens in the year 2185 aboard a Cerberus space station, a research facility of Project Lazarus, which fell under attack by hacked security mechs. After the Commander aids Cerberus agents Miranda Lawson and Jacob Taylor in escaping, Shepard is taken to a headquarters of Cerberus and granted an audience with the Illusive Man, who explains that Shepard was revived and "upgraded" in return for the Commander’s aid in combating a new threat in which human colonies have been attacked, their colonists deemed missing.

Due to the ignorance and political red tape hampering both the Alliance and the Council, Cerberus is the only organization in a position to combat the threat, and Shepard reluctantly agreed to work with them to solve this threat, even though he didn’t trust Cerberus or the Illusive Man.

Shepard and the team are dispatched to investigate the recently attacked colony of Freedom’s Progress, located in the Terminus Systems. There, the group encounters Tali’Zorah vas Neema, one of Shepard's former squad members, and discovers that the mysterious insect-like humanoid bipeds known as the Collectors were behind the attack and are responsible for the further abductions of other human colonies. Shepard reports this to the Illusive Man, who then places him in command of the Normandy SR-2, a larger second generation ship modeled after the original Normandy SR-1. With the guidance of the Illusive Man, Shepard begins traveling across the galaxy to recruit a new team for what is assumed to be a suicide mission.

Meanwhile, rumors of Shepard’s apparent survival have mixed concerns. Some would even think that Shepard is undercover investigating the colony disappearances.

Forming a new squad
The Illusive Man initially provides Shepard with four dossiers regarding potential recruits: a salarian scientist, a mysterious vigilante called Archangel, a krogan warlord, and a powerful but psychotic biotic. The salarian, Mordin Solus, is found on Omega and is working to stop a plague engineered by the Collectors but distributed throughout Omega by the vorcha. The vigilante Archangel is also on Omega, holding out on his own in a battle against three mercenary gangs: the Blood Pack, Blue Suns and Eclipse. After reaching Archangel's hideout, Shepard learns that Archangel is actually Garrus Vakarian, one of Shepard's previous squad members. Garrus is seriously injured while battling the mercenaries, and, although he is permanently disfigured, he survives and joins the team. The krogan warlord, Okeer, is found attempting to create the perfect krogan through unethical genetic research. When the warlord is killed, he leaves his creation, Grunt, under the care of Shepard. The biotic, Jack, revealed to be a woman, is also known as "Subject Zero." Cerberus arranges for her to be purchased from the prison holding her; Shepard travels to the Purgatory prison ship. Once there, however, Shepard is betrayed by the warden as he attempts to capture Shepard for a bounty. Shepard manages to escape the trap and rescue Jack, who joins the team despite an initial distrust of Cerberus operatives.

After the recruitment of the four squad mates, the Illusive Man reveals that a human colony called Horizon has come under Collector attack, and he dispatches the team in an attempt to save the colony. He also notes that one of Shepard's surviving crew members, Ashley Williams, is stationed at the colony to oversee the construction of massive defense towers. Shepard arrives with his team and battles the Collectors face-to-face; the group appears to have arrived too late as half of the colonists have already been taken away. Shepard's team is able to activate the colony's defense cannons and turn them on the Collector ship, which then flees the planet under heavy fire. Shepard later reunites with his former lover, who leaves feeling betrayed by Shepard working for Cerberus.

After returning to the Normandy, it is revealed that the Illusive Man allowed the Collectors to attack Horizon by leaking a tip to the Alliance that Shepard is alive and working with Cerberus. The Collectors intercepted this message and attacked the colony. The Illusive Man suspected the Collectors were looking for Shepard or people connected to him. It soon becomes clear that the Collectors are targeting Shepard. He is provided with dossiers on three more potential recruits: an asari Justicar, a drell assassin, and Tali. Shepard finds the Justicar, Samara, on Illium. She joins the team after Shepard investigates the Eclipse mercenary group and its involvement in a murder. The drell assassin, Thane Krios, is also found on Illium and is in the midst of completing an assassination contract on Nassana Dantius. After learning of Thane's next target, Shepard fights resistances along the way to the top floor of the tower complex where the target is located. Shepard encounters Thane, who successfully dispatches his target and joins the team, as Shepard can provide him with a purpose. Tali was found on a geth-occupied quarian colony world, Haestrom, where she is researching the system's rapidly dying sun. After she is rescued from an immense geth force, she agrees to join Shepard’s team.

Investigating the Collector Ship
"Shepard, we caught a break. I intercepted a distress call from a turian patrol. They stumbled on to a Collector ship beyond the Korlus system. The turians were wiped out, but not before they crippled the Collector vessel. I need you to board that ship and get some hard data on the Collectors. Find us a way to get to their homeworld."

- The Illusive Man to Shepard

Although the Illusive Man had still been assisting Shepard as they both worked to stop the Collectors from further threatening human colonies, their relationship had clearly suffered since Horizon. The Illusive Man informs Shepard that a turian patrol engaged a Collector ship, and managed to disable it before being destroyed, and that the Normandy should take the opportunity to investigate the ship before the turians respond, and find any data or technology that can help them on their mission. Upon boarding the ship, Shepard discovers many empty collector pods, as well as the bodies of dead human colonists, apparently subjected to various experiments by the Collectors. Shepard then discovers that the Collectors had also been experimenting on their own, with EDI saying that they appeared to be researching their own genetic similarity to humans. EDI's genetic analysis of the deceased Collectors reveals that they are in fact the long extinct Protheans, having been subjected to extensive genetic modification to alter them for the Reapers' purposes.

As Shepard proceeds deeper into the ship, Joker discovers that it is in fact exactly the same Collector vessel responsible for the attack on Horizon and the destruction of the original Normandy, which Shepard remarks is far too uncanny to be a coincidence. When Shepard's team reaches the center of the ship, they discover that it contains millions of empty pods, more than enough to hold every human in the Terminus Systems, thus indicating that their ultimate target must be Earth. Shepard is able to link EDI with the Collector ship's systems in order to search for any useful information, but she is quickly interrupted as she discovers that the ship is not disabled, and the Collectors have drawn the Normandy into a trap. EDI also reveals that the Illusive Man knew all along that the "disabled" Collector ship was a trap but still sent Shepard and the Normandy to the ship in order to gain information. Shepard and the squad fight their way out and escape from the ship on the Normandy before the Collector vessel can bring its weapons to bear.

After escaping, Shepard confronts the Illusive Man, who admits to sending the Normandy into an obvious trap in order to gain information, and says that it was necessary in order for the Collectors to believe they have the upper hand and telling Shepard about it would have tipped the Collectors off. This to Shepard was an unnecessary risk not only to him, but to the entire squad who went there. The Illusive Man countered that with Shepard’s actions they had finally found the key to travelling to the Omega-4 Relay. After talking his way out of the argument, the Illusive Man reveals the data gathered by EDI has led to the discovery of the Collector's means of traversing the Omega-4 relay, an advanced Reaper IFF system. Furthermore, the Illusive Man showed no remorse, undermining Shepard’s trust in him. EDI is also able to calculate the location of the Collector homeworld from their ship's navigational data, and reveals it to be within the galactic core, an extremely dangerous area, which likely accounts for the fact that no ships ever return from the other side.

Obtaining a Reaper IFF
"The Reapers and Collector ships use an advanced identify Friendly/Foe system that the relays recognize. All we need to do is get our hands on one of those IFFs."

- The Illusive Man to Shepard

The Illusive Man then reveals that Cerberus has located a derelict Reaper orbiting a remote planet, evidently destroyed millions of years beforehand, and sent a science team there to recover the device required to pass through the Omega 4 Relay—a Reaper IFF transponder. During the course of the investigation, Shepard discovers that the Cerberus science team members had all been killed before their arrival. Video logs left by the science team make it evident that even though the Reaper is no longer sentient or functional; the indoctrination effect that emanates from all Reapers is still present. The derelict ship automatically activates its shields, isolating Shepard's team from the Normandy and thus making their only means of escape to destroy the ship's power core, which is also powering the ship's latent mass effect fields and preventing it from plunging into the planet below. Battling their way through the husks on board, Shepard and the team are assisted by a single geth, somehow able to talk and also apparently friendly. Shepard and the team recover the IFF and fight to the core of the ship, where the mysterious geth assists them once again before being disabled. As the Reaper's core is destroyed, its shields disappear and Shepard's team is able to escape to the Normandy before crashing into the planet, along with the disabled geth. Following the mission, Shepard activated the geth, who is named Legion by EDI and joins the team against the Collectors.

Shortly after, Shepard departs with the recruited members on a shuttle towards their next mission as the Normandy prepares the IFF for testing in their absence. However, EDI discovers a hidden signal after activating the IFF, and realizes that the IFF is broadcasting the Normandy ' s position. This turns out to be another trap set by the Collectors, as their ship is able to surprise the Normandy with Shepard's entire team absent. Collectors board and seize control of the ship, and Joker is forced to give control of the ship over to its on-board AI, EDI—a potentially dangerous move. After successfully regaining control of the ship, EDI manages to pilot the Normandy away from the Collectors and rid the ship of all enemies, but the entire crew except Joker is taken by the Collectors. Upon returning to the ship, Shepard's hand is forced—the Commander decides to go through the Omega-4 relay immediately to rescue the Normandy crew members.

Beyond the Omega-4 Relay
"The Collectors attacked our ship. They took our crew, our friends. They think we’re helpless. They’re wrong. They started a war, but we’re not here to finish it. We’re here to make them regret – to show them and everyone else what happens when you go too far. No more running, no more waiting. Let’s hit them where they live."

- Shepard rallying his squad for the attack on the Collector’s main base of operations

Eventually, Shepard decides to travel through the Omega-4 Relay. When he proceeds, the Normandy activates the Reaper IFF and engages the Omega 4 Relay. Upon exiting the far side of the relay, the Normandy appears in the midst of a vast debris field containing the wreckage of thousands of ships, presumably all destroyed attempting to traverse the relay. The Collectors have stationed automated defenses in the debris field known as Oculus, which the Normandy fights off. After defeating the Oculus and reaching the far side of the debris field, the Normandy discovers the Collector base, a giant space station orbiting a black hole. The Collector Cruiser is dispatched from the station, and the Normandy engages and destroys it, but as it explodes the blast cripples the ship and causing it to crash land on the outer surface of the base. Fortunately for the squad, due to the various upgrades applied to the ship over the course of the mission, the crew suffered no casualties and the ship sustained minor damage while fighting the Oculus and Collector Cruiser.

Over the course of the rest of the mission, Shepard and the team enter the station and battle their way through the Collectors to the station's core, rescuing the surviving Normandy crew as they go. Upon reaching the heart of the station, they discover that the Collectors have been constructing a new human-like Reaper, made from the genetic material of the abducted humans and fused with the advanced technology of the Reapers. EDI hypothesizes that the Reapers attempted and failed to create a Prothean-Reaper, and instead enslaved them and turned them into the Collectors, and that they are now facilitating the Reaper equivalent of reproduction. EDI also guesses that due to its human appearance, Reapers are crafted to resemble the race from whose genetic material they are created. Shepard targets the weak supports of the contraption, which is in the very early stages of its construction, and it is seen collapsing into the lower confines of the area. Shepard then sets about with the plan to destroy the station.

At this point, the Illusive Man contacts Shepard and suggests that instead, use a radiation pulse be employed to kill all of the Collectors on board, but keep the station intact to allow Cerberus to research its technology. He notes that any information obtained from the Collector Base would be very valuable in the coming war against the Reapers, in addition to strengthening humanity's position in the galaxy against other races. Shepard refuses and decides to destroy the station, and Miranda, seeing the Illusive Man as a power-hungry madman, sides with Shepard over him and resigns from Cerberus, proving her loyalty to Shepard. After making the decision regarding the station's fate and initiating the countdown, the Human-Reaper resurfaces from the depths of the station and attacks Shepard's team. After Shepard and the team destroy the Reaper, the surviving squad members escape to the Normandy and leave.

Aftermath
"The mission was a success, and in the end, the whole team made it out alive. We stopped the Collectors, and we stopped the Reapers from creating their abomination. And we bought everyone just a little more time."

- Shepard's journal entry

Aboard the Normandy, Shepard contacts and converses for one last time with the Illusive Man, who is extremely angry with Shepard's idealism, saying he knew that Shepard would "choke on the hard decisions". He also asserts that the Collector technology could have been used to humanity's benefit, and claims that, given its goals, Cerberus is humanity. Shepard rebuffs the Illusive Man, who wasn't looking for his approval and informs him of his decision to leave Cerberus. The Illusive Man tries to dissuade the Commander, citing that it is because of him that Shepard is alive. Shepard then rudely terminates all communication, but not before promising that he’ll win the war against the Reapers without sacrificing humanity's soul.

As the Normandy undergoes repairs following the mission, little did the crew realize was that the Reapers had awakened from their hibernation in dark space and began their march towards the Milky Way galaxy.

An investigation
Not long after his newly acquired freedom, Shepard travels back to Illium to deliver intel to Liara. At first, Liara is seemingly delirious about the information for it appears to hint on the Shadow Broker's true location. In addition, the message contains information that Liara's former drell partner, Feron, is actually still alive and is probably being held hostage by the Shadow Broker. After a short conversation on the subject with the Commander, Liara leaves her office and tells Shepard to meet her at her apartment.

Upon his arrival, the Commander witnesses that the apartment is under investigation by Illium police, led by Spectre Tela Vasir, who dismisses the cops as Shepard enters the apartment. In response to Shepard's question regarding the unexpected investigation, Vasir explains there has been an attempt on Liara's life. She tells the Commander that she is unsure of Liara's current location and that she was unsuccessful in finding any clues; she invites Shepard to further search the apartment for clues. Eventually, Shepard finds what appears to be a backup disk, which is then played by Vasir and the Commander. The disk is found to contain a recorded conversation between Liara and a salarian contact by the name of Sekat, who explains that he has managed to pinpoint the Shadow Broker's location, and asks Liara to come to his office at Baria Frontiers in the Dracon Trade Center. Now that they have what they are looking for, Vasir and Commander Shepard travel to their next destination at Baria Frontiers.

The Truth
Just as the team arrives at the Dracon Trade Center, the three floors of the building are taken out by a sudden explosion, presumably an attempt to prevent Liara from receiving the information sought from Sekat. Vasir suggests that the Commander and the squad proceed inside while she takes off to the roof in order to seal off the building from the top. As Shepard and the squad enter the building, they find it to be a chaotic mess with dead bodies and wounded civilians all over the place. Tela maintains contact with Shepard to guide the Commander through. As Shepard proceeds to the upper floors into the Baria Frontiers Office, the Commander finds a clue that Liara has just signed in a few minutes ago, confirming that Liara is indeed in the building. Proceeding inside the office room for further exploration, Shepard and the team are blinded by a flash grenade, followed by a wave of enemies who immediately scatter around the area and open fire. Shepard quickly radios Vasir regarding the ambush, who tells the Commander that they are the Shadow Broker's private army and confirms their presence in the building. With no choice to fall back, Shepard and the team return fire, slowly but surely making their way through the small hallways of the destroyed office.

Eventually, Shepard and the squad reach their destination, where they see Sekat's dead body after he was shot by a Shadow Broker agent, who is then shot by Vasir herself. Vasir asks the Commander about Liara's body, and if Shepard located it. However, Liara emerges from the shadows, wielding her pistol at Vasir. Liara explains to Shepard that Vasir tried to assassinate her, broke into her apartment, and is the one that signaled the Shadow Broker's agents. She also remarks that Vasir is the one who killed Sekat and took his data, which is currently in her possession, revealing that Vasir is, after all, an undercover Shadow Broker operative. Exposed, Vasir shatters the glass with her biotics and makes a run for it. Shepard tries to tackle Vasir before she jumps out the now-broken window but fails to do so, causing the Commander to fall to the floor while Liara proceeds to chase Vasir, not bothering to look back at Shepard and the squad. Shepard is then attacked by more enemies emerging from the nearby Eldfell-Ashland Energy office who attempts to slow down the Commander so that Vasir can get away. Shepard and the team continue to fight their way through the resistance while pursuing Vasir out of the building. When they exit the building, the team finds Liara exchanging fire with Vasir at the parking lot. It doesn't take long before Vasir calls her X3M skycar and quickly jumps into it to fly away. Nonetheless, Liara finds a nearby vehicle, which she and Shepard use to chase Vasir through the skies of Illium.

At the end of the chase, Shepard and Liara manage to catch Vasir, whose vehicle has crashed on the roof of the Azure Hotel. Although they don't actually have her yet, they can make their way to the other side of the roof where she most likely is. Coupled with the fact that Vasir is now wounded due to the crash and is thus slow, Shepard and Liara have a much better chance of capturing her this time. However, as the team lands and exits the vehicle, reinforcements arrive and start shooting at them. After the battle on the roof, Shepard and Liara continue running inside and emerge to the other side of the roof, where they spot Vasir's footsteps and follow them until they reach Vasir and aim their pistols at her, hoping she surrenders. Even though she is badly injured, Vasir grabs a random hostage to use as leverage against Shepard and Liara. The situation is quickly dealt with, and the hostage escapes, but Vasir, not about to give up just yet, starts attacking the squad with everything she has. At the end of the battle, Vasir drops to the floor, allowing Liara to pick up the data disk. Vasir protests to Shepard's remarks she sold out the Council, insisting she is nothing like Saren and claiming that the Shadow Broker is powerful and her work with him has helped save lives and kept the Citadel safe, and that she believes in sacrificing a few for the greater good. She also brings up the Commander's involvement with Cerberus and tries to judge Shepard for it, before she takes her last breath. Shepard then heads back to Liara, who is examining the disk, to have a conversation with her, which, among other things, involves the Shadow Broker's intention of wanting to kill Liara all along and at any cost. In any case, with the data in their possession, Shepard and Liara travel to the Shadow Broker's location for their primary objective.

Assault on the Shadow Broker's Base
The data obtained reveals that the Shadow Broker settles on the planet Hagalaz, in the Sowilo system of the Hourglass Nebula. Specifically, the Shadow Broker lives onboard a massive ship that travels through the thick, erratic atmosphere of Hagalaz. Shepard, Liara, and a third squad member take the shuttle from orbit down to the planet. Liara provides Shepard with valuable input on the planet's atmosphere, the ship, and the general plan of the mission. First, they have to find a hatch that leads to the inside of the ship, where Feron is held. The shuttle lands, and Shepard and the team begin finding their way for a hatch to get inside. The weather is dreadful, and the layout of the ship's exterior isn't exactly easy to navigate through, but they proceed anyway. Shortly following their touchdown, the team is engaged by maintenance drones, which Liara presumes is because the drones think the team is debris from the storm. After that, troops from the Broker's army start coming and attacking the squad as they advance through. Shepard and the team continue advancing until they reach a door that allows them in. However, the door is locked, but Liara tries to hack it with a certain hacking device, which she says will take a while before the door is completely hacked open. Waiting for the door to open, the team has to defend the position from numerous waves of Shadow Broker forces. Eventually, the door is successfully hacked and they run inside.

As the team makes their way inside, more troops are encountered. Liara remarks she has downloaded the ship's layout, saying that they're heading towards the prison block, where Feron is supposedly located. Continuing to the prison block and fighting their way through, the team reaches a locked door that leads directly to where Feron is. They bypass the door and enter to find Feron. Liara attempts to release the drell, but instead, he is shocked. Feron explains that his current status makes him unable to be pulled out, otherwise his brain will fry. Shepard states that this "looked too easy" and asks Feron regarding the Shadow Broker, but unfortunately, Feron can't say much, either, since even that gets him shocked. At this point, Liara and Shepard decide that their only option is to confront the Shadow Broker himself and put an end to all this. They walk out the prison block, facing more enemies along the way. At last, they make it to the Shadow Broker's office.

Storming the Shadow Broker's office, where he calmly awaits them behind his desk, Shepard and the team find that the Shadow Broker is a species never encountered before. Not bothering to get up, the Broker coldly asks if Shepard and Liara are here for Feron, noting Shepard's actions are reckless even considering the Commander's history. After a brief word exchange between Shepard and the Broker, Liara demands Feron, to which the Broker responds by reminding Liara that her own actions are what caused this to Feron. Knowing that the Commander had defeated the Collectors, the Broker announced his intention to use the Normandy SR-2's IFF to salvage remaining Collector technology. The Broker notes the team's third squad member (commenting on the financial/political benefits their capture/death will bring him) while arrogantly disregarding Liara, telling her that he knows all her secrets. In response, Liara tells the Broker that he is a yahg, likely taken from his homeworld as a trophy or pet, when he ended up killing the original Shadow Broker and taking his place some 60 years ago. This enrages the Broker, causing him to smash his desk and throws it at the three people standing in front of him, knocking out the third squad member, leaving only Liara and Shepard against him.

The two rely on each other to fight the giant yahg, in what seems like an unwinnable battle at first. At some point during the fight, Liara suggests that Shepard distracts the Shadow Broker while she prepares for an attack. As soon as Shepard provides the distraction, Liara uses her biotics to pull down the liquid in the above tank straight onto the Broker, which causes the Broker's barrier to malfunction and explode, ultimately destroying him for good.

Aftermath
The battle causes the Broker's agents to radio his office asking for immediate updates on the situation. At first, Liara seems overwhelmed and unsure what to do. Then, she moves toward the panel and responds to the agents using the Shadow Broker's voice modification to avoid exposing herself, saying that the situation is under control and it was merely a hardware problem that disrupted communications momentarily, ending the message by requesting the agents to resume standard procedures and that she wants an update on all operations within a solar day. Feron comes to the room and quickly pulls his pistol, before he realizes everything has been dealt with. Liara explains that she is now the new Shadow Broker, believing that it is something she has to do. Feron leaves with the other squadmate to check on the power system, leaving Liara and Shepard by themselves.

Shepard comforts a crying Liara with a hug, who is happy that her revenge is finally over after two years' worth of struggling. Liara thanks him for what the Commander has helped her accomplish and assures that he is welcome any time. In a subsequent conversation, Liara will remark that her role as the Shadow Broker will likely play key role in the upcoming war against the Reapers. She also provides Shepard with additional insight on the Shadow Broker's plans and what he knew. Later, Shepard invites Liara to the Normandy for a catch up.

Destruction of the Bahak system
"Just this morning I received word that the batarians arrested her. They’re holding her in a secret prison outpost on terrorism charges. I need you to infiltrate the prison and get her out of there. As a favor to me, I’m asking you to go in alone."

- Fleet Admiral Steven Hackett to Shepard, about Dr. Amanda Kenson

Eventually, Shepard was approached by Fleet Admiral Steven Hackett, asking him to locate and rescue one of his close personal friends, Dr. Amanda Kenson, an Alliance deep-cover operative in batarian space who has come across evidence that a Reaper invasion is imminent. Hackett explains that Kenson was recently captured by batarians and charged with terrorism. Wanting to avoid a diplomatic incident with the Batarian Hegemony, Hackett requests Shepard to go in alone and rescue the scientist as a favor. Shepard agrees to help and uses the coordinates given by Hackett to travel to the batarian prison on the planet Aratoht where Kenson is being held.

Landing outside the prison, Shepard makes it past several security measures and prison guards. He locates Kenson in the middle of an interrogation and frees her. Shepard and Kenson fight past more guards and escape on a batarian shuttle. On the way to Kenson's team's base, she reveals that she and her team had entered batarian space to investigate rumors of Reaper technology orbiting on the fringes of the Bahak system. The team discovered a Reaper artifact they dubbed "Object Rho" hidden in the asteroids near the system's mass relay, and learned from it that the Reapers were rapidly approaching. The Reapers could use the system's mass relay, the "Alpha Relay", to strike anywhere in the galaxy. Kenson and her team started what they called "the Project" to prevent this from happening. Their plan was to hurl a large asteroid at the Alpha Relay and destroy it, delaying the Reapers' plans by months or even years as they are forced to find another relay. A consequence of this plan would be that the relay's supernova-like explosion would obliterate the Bahak system and kill the 300,000 inhabitants of Aratoht. Since the stakes are so high, Shepard insists on seeing Kenson's evidence first. Kenson agrees and informs her team at the Project Base that she and Shepard are en route.

At the Project Base, Shepard notices a numeric readout above the hangar gateway. Kenson says that the readout is a countdown to the Reapers' arrival; in two days, the Reapers will be at the Alpha Relay. The countdown itself is based on pulses emitted by Object Rho. The pulses are reactions to the Reapers' proximity and the intervals between them have been decreasing steadily. In little over 48 hours, the pulses will become constant and the Reapers will have arrived. As Kenson leads Shepard to Object Rho, she explains that "the Project" is ready to go. The team hasn't been debating if it could be carried out, but rather if it should be. The Reapers will arrive regardless, but without the shortcut that the Alpha Relay provides, they would be forced to spend months or even years more traveling to another relay.

At the lab, Kenson presents Object Rho to Shepard. The Commander becomes wary after seeing that the Reaper artifact is sitting in the open. Kenson tells Shepard to wait for the artifact to show Shepard a vision which will prove that the invasion is real. Shepard is overcome with the vision, which shows dozens of Reapers speeding towards a mass relay. Suddenly, Kenson pulls a gun on Shepard and says she can't let the Commander stop the Reapers; Kenson and her team had been indoctrinated by Object Rho. Shepard disarms Kenson, who escapes and locks him in the chamber as it is swarmed with guards. Shepard fights as long as possible, but is eventually overwhelmed and incapacitated.

Shepard awakens two days later in a medical lab in Project Base, to the surprise of the monitoring medic. Shepard disables two guards, but is locked in the room by the medic. At a nearby terminal, the Commander takes control of a LOKI Mech outside, which Shepard uses to kill the scientist and break the mechanism that seals off the room. Shepard suits up and advances through the Project Base, intending to complete "the Project" before the Reapers arrive in less than two hours.

The Commander fights through Kenson’s indoctrinated security guards to reach the control center and prepares to activate the Base's engines. After being warned by the Base's VI that initiating the Project will kill all of the Bahak system's 304,942 colonists, Shepard confirms the order. The engines ignite and the asteroid accelerates toward the Alpha Relay. Dr. Kenson interrupts Shepard's attempt to access communications, threatening to overload the Base's fusion core to stop the Project. Getting to the core, Shepard manually initiates cooling systems to stop Kenson's crazed plan. In the core chamber, Kenson laments not being able to hear the Reapers' whispers anymore and witness their coming to the galaxy. When she raises a bomb detonator, Shepard tries to talk her down, but Kenson still presses the button and dies in the explosion, which also incapacitates Shepard.

When Shepard recovers, the asteroid is now minutes away from colliding with the Alpha Relay. Commander Shepard races to the Project Base's shuttle landing pads to escape, but is too late; the last of the shuttles lifts off and speeds away, leaving behind other Project personnel. Shepard eliminates them and finds a communications uplink nearby. While calling the Normandy, Harbinger appears via a hologram projector and tells Shepard that the fall of the galaxy's civilization is inevitable. Before disconnecting, Harbinger tells Shepard to "prepare for the arrival." The Normandy makes its approach and Shepard lands a running jump into the airlock. Seconds before the asteroid hits, the Normandy escapes the Bahak system through the relay. As anticipated, the relay is destroyed and the explosion obliterates the system.

Sometime later, Admiral Hackett boards the Normandy to debrief Commander Shepard in-person. Hackett wants Shepard to explain why a simple rescue mission ended with the destruction of a batarian system. Shepard confirms that Dr. Kenson's proof of the Reaper invasion was real, and the invasion had been only days away. The Commander had no choice but to destroy the Alpha Relay, despite how this would doom the batarian colonists. Hackett is satisfied by Shepard's story, saying he would give a medal to Shepard for this, but reveals that tensions between the Systems Alliance and the Batarian Hegemony were running high; the batarians might start a war over Shepard's actions. He was then a wanted man, gaining the status of a war criminal, while Admiral Hackett admitted he saw him as a hero he told Shepard he would eventually have to give himself up. Everyone knew about the Reaper threat, but nobody had seen the things that Shepard, Hackett and Anderson had seen. Before leaving, Hackett warns that at some point, Shepard will have to face trial over this incident on Earth.

Imprisonment
"I've already lost count of the days since they relieved me of duty. Strange how years of your life can just vanish in the blink of an eye. Then in a flash, you've got nothing but time. Time to reflect on everything that's happened. Hard to believe it's only been a few years since this all began."

- One of Shepard's audio logs

Following the suggestion of Admiral Hackett, Shepard turned himself into Alliance custody and was stripped of his rank and imprisoned in an Alliance base in Vancouver under house arrest. Negotiating with the Alliance, while losing the Normandy in the process, Shepard remained on Earth awaiting a scheduled trial regarding his association with Cerberus and the destruction of the Bahak system. During his incarceration, Shepard was confronted by Corporal Toombs, now a mercenary, who proceeds to inform him that he is subject to his policy of killing any and all Cerberus operatives he encounters and orders his men to kill the commander. Shepard was able to hold off his attackers, incapacitating two of them and breaking Toombs’ right arm, before security guards arrived and broke up the fight before it escalated.

Fall of Earth
Six months have passed since the destruction of the Bahak system and Shepard’s voluntary return to the Alliance. The Commander has since been relieved of command and detained in a Systems Alliance facility in the city of Vancouver on Earth. Without warning, Alliance deep space outposts beyond Sol began to go dark. Fleet Admiral Steven Hackett, the head of the Alliance military, begins to prepare for an imminent invasion. Admiral David Anderson arrives in Vancouver and escorts Shepard with Lieutenant James Vega to a meeting with an Alliance defense committee. Shepard confirms their worst fears: the Reapers have returned to the galaxy and are on their way to Earth.

At that moment, contact is lost with Luna Base and news reports begin to surface of an unknown alien force landing in Earth's cities. The Reapers have already arrived. A Reaper capital ship then descends through the clouds over Vancouver and blasts the Alliance building, killing the defense committee and Alliance staff. Shepard and Anderson survive and contact Lieutenant-Commander Ashley Williams, telling her to get to the Normandy.

As Shepard and Anderson make their way from building to building to get to the spaceport, Anderson tells Shepard that they have to get to the Citadel and seek help from the Council. They reach a comm set near a crashed gunship and hail the Normandy to evacuate. After holding off an attack from Cannibals, the Normandy bombs the area clear of attackers. As Shepard boards the ship, Anderson informs the Commander that he will stay behind to lead the resistance and hands over Shepard's dog tags. Shepard protests, but Anderson charges Shepard with getting as much help as possible to save Earth and stop the Reapers.

As the Normandy lifts off, Shepard witnesses a child running to an Alliance evacuation area and boarding a shuttle. As the shuttles lifts off, a Destroyer-class Reaper emerges from behind a cluster of buildings and targets the shuttles, killing those who were aboard including the child. Distraught, Shepard steps away from the open shuttle bay doors of the Normandy, and the ship escapes Earth as more Reapers and the wreckage of Alliance ships rain down upon the planet.

Mars Archives
"I’ve discovered plans for a Prothean device. One that could wipe out the Reapers."

- Liara T'Soni

Shortly after escaping Earth, Shepard received a communication from Admiral Hackett, ordering the commander to the Prothean Archives on Mars, where humanity first discovered mass effect technology. Hackett insists that Liara T'Soni has found there what may be the only way to defeat the Reapers.

Upon arrival, Shepard, James and Ashley take the shuttle down to the planet, receiving a warning from EDI that the base is not responding. They soon discover the reason why upon witnessing Cerberus soldiers executing Alliance personnel; the group fights their way through the enemy, inferring from the small size of the Cerberus force that they must have had help from the inside. Ashley expressed her surprise that Shepard was unaware of this, given his past association with Cerberus, and was unwilling to believe he cut ties with the extremist organization following his defeat of the Collectors, only to receive an angry rebuttal from Shepard -- who apparently has had enough of her mistrust towards him and constantly questioning his loyalty.

After entering the station and arriving in time to witness Liara biotically overpower and execute her pursuers, who later explains why Hackett sent them to find her; she has found in the Archives blueprints for a Prothean device that might allow them to turn the tide against the Reapers. Unfortunately, Cerberus has learned of it too, and now they must hurry to recover the necessary information before Cerberus can. Sending James back to the shuttle to secure their escape route and prevent Cerberus from doing so, Shepard, Ashley and Liara fight their way through the station to the main Archive, discovering along the way the identity of the traitor in the station: Dr. Eva Coré, supposedly a recently arrived researcher, but in truth a mole who sabotaged the station's defenses to allow Cerberus entry.

Reaching the Prothean beacon at the heart of the Archives, the Illusive Man contacts them by hologram, mocking the Alliance for failing to take advantage of the wealth of information the Protheans left behind and commenting that Shepard is fighting a losing battle. He also explains his new motivation: to find a way to control the Reapers and thus use their power to advance humanity to a new level of evolution and above the other races. Deriding the Illusive Man's plan as madness, Shepard vows to use the information to destroy the Reapers and dismisses the Illusive Man's warning not to interfere in Cerberus's plans.

The group then encounters Dr. Coré, who had been trying to upload information on the Prothean device, but her upload is interrupted by the squad and she tries to flee. Although Coré is able to reach a Cerberus shuttle, James disables it with a kamikaze attack before it can escape, having also alerted the Normandy to extract the squad. Coré, revealed to be an android by the explosion, emerges from the wreckage and attacks, critically injuring Ashley before being disabled by Shepard. The Normandy arrives to extract the team just as Reaper forces begin landing on Mars.

Having escaped Mars, Shepard forwards information on the Prothean device to Hackett, orders Liara and EDI to begin extracting intel from the android and orders the Normandy to the Citadel.

Uniting the galaxy
"Build alliances. Gather everything and everybody you can for the cause."

- Fleet Admiral Steven Hackett to Commander Shepard

Upon arrival at the Citadel, Ashley is taken for medical treatment at the nearest hospital and Shepard conveyed to a meeting with the Council. Upon arriving, Shepard is quick to see the Councilors are looking to their own borders. Despite Councilor Udina's insistence that Earth is bearing the brunt of the attack and needs the most help, Councilor Tevos succinctly sums up their view: while the Reapers focus on Earth, the other races have time to regroup and build up their own defenses. The Council is also unimpressed by the Prothean device, insisting it must be flawed as it failed to save the Protheans from extinction at the hands of the Reapers, but Liara explains that a missing component referred to as "the Catalyst" prevented its completion. All is not entirely lost for Earth, however: Councilor Valern informs Shepard of a war summit they are convening to properly organize their strategy against the Reapers, and that whatever the summit decides will give the final word on the deployment of Council forces.

Upon departing the meeting, Shepard and Udina are met in the human Councilor’s office by Councilor Sparatus, who explains that Palaven's ruler, Primarch Fedorian, was to head the war summit, but didn't escape the system before the Reapers arrived. He requests that the Normandy extract him from his current location on Palaven's moon Menae, explaining that Fedorian will be a useful ally in accruing support for Earth. Before departing, the turian Councilor informs Shepard that the Council has agreed to uphold his Spectre status, granting Shepard the benefits of the position.

The Normandy enters the turian home system to find Palaven and Menae under heavy attack by the Reapers, with the turian military under immense pressure and taking heavy losses. Upon landing on the moon at a turian base, Shepard learns from General Corinthus, the commanding officer of Menae’s moon base, that Primarch Fedorian is dead, having been killed an hour before Shepard's arrival and they have no idea who has succeeded him because their communications with Palaven Command have been cut. Fighting through swarms of Husks to the comm tower and repairing it, the group soon learns that General Adrien Victus, a popular military commander with "a reputation for playing loose with strategy", has been named as Palaven's next Primarch; however, he is fighting at a base several miles away, with which radio contact has been lost. At the same time, Shepard receives a message from Joker that EDI and the Normandy are acting strangely; Liara returns to investigate, while Shepard's old squad-mate Garrus Vakarian, now named strategic advisor to the turian army, greets Shepard and joins the team to help fight and to lead them to Victus' position.

Fighting their way through Reaper forces, Shepard, James and Garrus arrive at the base and after helping Victus and his soldiers defeat their attackers, relay the news to the General that he is the new leader of his people. Victus is doubtful about his ability to lead, claiming to be no diplomat and unwilling to leave his men, but he reluctantly agrees to accompany Shepard to the summit. He insists he can't divert troops to Earth until Palaven can be secured, something beyond the turian military's ability to do now. The turians will need reinforcements, namely the krogan, to succeed, and Victus insists they will have to be at the summit.

Upon returning to the Normandy, Shepard and the crew discover the earlier power fluctuations were caused by EDI implanting herself in Eva's body, a process which has completed successfully and given EDI more options, namely the ability to leave the Normandy and accompany Shepard into combat. Soon after, Shepard receives word from Admiral Hackett that Alliance Research and Development has begun construction of the Prothean device, dubbing it "Project Crucible".

The last Prothean
"I will help you fight. And the last thing the Reapers hear before they die will be the last voice of the Protheans sending them to their grave."

- Javik to Commander Shepard

Shepard later received a message from Alliance Command learning that Cerberus attacked Eden Prime and is occupying the colony, but in the process, Cerberus uncovered a major Prothean artifact. Alliance HQ ordered Shepard to infiltrate the colony and recover the artifact.

After being dropped off, the squad proceeds down the pathway until reaching their first set of buildings. Once obtaining intel for the Eden Prime resistance movement, Shepard activates the excavation lift and the group discovers from Liara that Cerberus uncovered a living Prothean in stasis, but if they open the pod without the proper signal it will kill the Prothean inside. To activate the pod, the group needed the command signal to open it, and the stasis readiness signal to deactivate its stasis mode. Since both were located in disparate locations on the settlement, a Cerberus shuttle flies overhead and drops off several combat engineers, troopers, and centurions to delay Shepard’s team.

The team enters one of the buildings that Cerberus was using to study the footage of the Protheans in order to figure out how to open the pod. Fortunately, due to the Cipher he received on Feros three years ago, Shepard was able to understand the footage detailing the Reapers’ invasion of the Prothean Empire. Once obtained, the group moves across the courtyard and enter a building with four corpses. Shepard remarks that the inhabitants were killed while "watching the game." Once outside, two Cerberus shuttles race overhead and drop additional troops and engineers, but are quickly swept aside. The group enters the second building and use to computer console to retrieve the information about how to physically open the pod.

Once the Cerberus troops present were eliminated, Shepard activates the pod and the Prothean awakens from stasis. He reacts with a biotic attack against his rescuers as he stumbles out of the pod, disoriented. He then looks up with shock at the human settlements, lush fields, and the ruins of the Prothean structures. Shepard then touches him, causing the Commander to experience his recent memories while he in turn quickly understands human language with his sensory ability. The Prothean introduces himself as Javik and agrees to join Shepard in destroying the Reapers, vowing he will not rest until the last Reaper is dead. However, he did not hide his surprise that "primitive" races the Protheans once studied are now the dominant galactic power.

Aiding the krogan
"Commander, I appreciate your need for our fleets, but I can't spare them. Not while my world is burning. But if the pressure could be taken off Palaven...''" "That's a pretty tall order." "''We need the krogan. I can’t see us winning this thing without them. Get them to help us, and then we can help you."

- General Adrien Victus and Commander Shepard

The decision to involve the krogan in proceedings causes major problems; the asari pull out of the summit altogether, believing turian-krogan relations too fragile for anything to be accomplished. A diplomatic meeting is held between Shepard, Primarch Victus, Dalatrass Linron (the leader of the Salarian Union), and Urdnot Wrex (the clan chief of the krogan). The dalatrass is openly hostile and insulting to the krogan leader, who is ambivalent to the plight of the turians, insisting that the Reapers are moving on Tuchanka and refuses to provide military assistance unless his own demand is met; that a cure is created for the genophage. The dalatrass flatly refuses to agree to such a demand, arguing that what Shepard and Victus are planning to do in curing the genophage is the same rash mistake the salarians made when they uplifted the krogan to fight against the rachni, while Victus believes the plan impossible because it would take years they don't have to synthesize a cure.

However, Wrex reveals intel he has received that following the experiments of a salarian scientist into curing the genophage on infertile krogan females, an STG team rounded up the survivors of the experiments – a group of now fertile females who are also immune to the genophage – and took them off-world. The dalatrass, under pressure, reluctantly reveals that the females are being held at an STG base on Sur’Kesh and accedes to their release, though she insists that curing the genophage will have dire consequences for her people and the galaxy as a whole.

Shepard, his squad and Wrex arrive on Sur'Kesh to oversee the exchange, meeting up with the salarian scientist in charge: former teammate Mordin Solus, who is responsible for the krogan females’ care and is revealed to be the source who leaked information on their existence to the krogan. However, as a side effect of the cure, the females suffered from weakened immune systems and only one has survived. A Cerberus strike force hits the base shortly during the exchange, seeking to kill the surviving female and stop any hope of a cure for the genophage. Shepard and his squad are forced to fight off Cerberus troopers deploying into the base as Mordin and Wrex attempt to extract her.

The team escape Sur'Kesh with the female krogan, who is christened "Eve" by Mordin, and the cure is rapidly developed. Eve takes some time to regain her strength, and when she’s ready Mordin proclaims her fit for travel to Tuchanka, where she’s needed for the last leg of the genophage cure’s completion. Wrex and Primarch Victus approach Shepard with problems of their own, requesting that the Commander deal with them if there’s time.

The Normandy then deploys to Tuchanka (recapturing an ancient ground-to-space cannon from Cerberus and preventing the terrorist organization from detonating an ancient turian bomb along the way), where the Reapers have begun attacking in force. They decide to release the cure from the Shroud, an enormous salarian structure built to repair Tuchanka's atmosphere that was then secretly repurposed to spread the original genophage. En route, Shepard is contacted privately by Dalatrass Linron, who insists Shepard cannot go through with the genophage cure and reveals that the Special Tasks Group sabotaged the Shroud years ago to prevent it from being used for such a plan. The dalatrass offers Shepard a deal: prevent repairs to the Shroud, thus causing the cure to fail, and in exchange, the salarians will provide military support and technical expertise to help construct the Crucible. Shepard and his team set course for Tuchanka to help cure the genophage, but the words of the dalatrass begun to weigh heavy on his mind.

Upon arrival on the planet, Wrex rallies the krogan forces, who will work with a turian fighter squadron to distract a Reaper destroyer using the Shroud to further poison the atmosphere of Tuchanka. However, the plan almost immediately goes awry, with the krogan ground forces delayed and the fighters decimated as they attempt to attack without support. The ground forces are scattered and Shepard’s team is forced to detour through ancient and impressive krogan ruins, that also happens to be home of the largest known thresher maw. They improvise a new plan, luring the thresher maw into attacking the Reaper Destroyer to buy them time. This strategy is significantly more effective than the last; despite overwhelming Reaper opposition, Mordin and Shepard make it to the Shroud and Kalros manages to kill the Destroyer. While en route, Shepard warned Wrex, Eve, and Mordin of Dalatrass Linron’s sabotage of the tower and told them how she wished for him to lie to his friends in order to gain salarian support. Wrex and Eve were eternally grateful for Shepard’s warning; while Mordin didn’t seem so surprised the Dalatrass would try to pull such an underhanded move.

However, new complications arose. Mordin, now aware of the STG sabotage, explains that the sabotage must be counteracted from the top of the tower in order to ensure proper release of the cure; a task that, with the tower collapsing as they speak, is essentially a suicide mission. Shepard regretfully allows Mordin to travel up to the top of the Shroud Tower to spread the cure. Mordin is killed in the subsequent explosion, finally at peace with his work on the genophage modification project. The Shroud lets out a blast of particles, blanketing Tuchanka with a shower of the cure before disintegrating and Eve survives the procedure, fleeing to a safe place alongside Wrex. Shepard succeeded in securing a krogan-turian alliance and only got a little salarian support from several strike teams within the STG, but dismissed the concern citing that the cost of their full-support was too high.

Cerberus coup attempt
"Get the word out: Udina’s trying to seize power!"

- Commander Shepard to Armando-Owen Bailey

Still feeling the effects of Mordin’s sacrifice following his mission on Tuchanka, Shepard is contacted by Councilor Valern, who requests a meeting on the Citadel regarding an important matter. The Councilor explains that it concerns Councilor Udina, who has been moving vast sums of money and the Councilor wishes to discuss where it is going, claiming that Shepard "won't like the news".

Upon arriving at the Citadel, however, the station is worryingly silent. Scanning emergency channels, the Normandy receives a transmission from an old associate of Shepard’s: drell assassin Thane Krios, who has retired to the Citadel to enjoy his remaining life, who explains that the Citadel is under attack; Cerberus has hit the station in overwhelming numbers and C-Sec is struggling to retaliate. The contact explains that Ashley (having recovered from the injuries sustained on Mars and been named a Spectre by Udina since then) has gone to protect the Council, while they are attempting to reach C-Sec Headquarters, since C-Sec cannot launch an effective counterattack while Cerberus holds it. Deploying in the shuttle, Shepard and his squad land in the middle of a pitched battle between C-Sec and Cerberus forces outside the headquarters, helping C-Sec Commander Bailey retake the office. Inside, Bailey uncovers intel that Valern was meant to be meeting with the Executor, presumably to have someone important prosecuted. Given the message the Councilor sent to the Normandy, Udina is implicated.

Reasoning that the Councilor is likely holed up in the Executor's office, a fairly defensible position, Shepard's squad fight their way through Cerberus' troops, but when they reach the office and extract the Councilor, they come under attack from Kai Leng, who is under orders from the Illusive Man to assassinate the Council. Valern also reveals that Udina is collaborating with Cerberus to stage a coup. Fortunately, Thane arrives and thwarts Leng's assassination attempt, but is mortally wounded in the process. Leng retreats to pursue the rest of the Council, with Shepard and company in hot pursuit.

Despite Leng's best efforts to slow down and stop his pursuit, Shepard reaches the Council ahead of him at a shuttle pad, locking the exits to prevent Cerberus troopers from getting in and a tense standoff ensues, with Ashley standing in his way. Shepard confronts Udina, the Councilors and Ashley about Udina's treachery. In response, Udina attempts to deny it and tries to frame Shepard to be in league with Cerberus. However, the rest of the Council recalled the last time they didn’t trust Shepard and after all the times they didn't listen to Shepard, begin to believe him. With the Council’s escape shuttle destroyed, Udina suggests overriding the lockdown, unaware that Shepard successfully convinced Ashley to stand down and get out of the way.

Udina, left with a few options, begins to override the lock on the door. Tevos tries to stop him, but he pushes her to the ground and pulls a gun on her. Shepard was ultimately forced to kill the human Councilor, followed by the arrival on scene of Bailey and C-Sec reinforcements. With Udina dead and their plan thwarted, Leng and the remaining Cerberus forces retreat, while C-Sec began securing the station.

Shepard was later present with Kolyat to visit Thane during his final moments at the Huerta Memorial Hospital, who recites a drell prayer of redemption intended for Shepard before passing away. Shepard says his final goodbyes to Thane, telling him that he won’t be alone for long.

Battle for Rannoch
"You’re throwing yourselves at the geth? Again?"

- Commander Shepard to Admirals Han'Gerrel, Zaal'Koris, Shala'Raan, and Daro'Xen

Following the coup attempt, efforts to speed the pace of the Crucible's construction and drive the Reapers back increase. Admiral Hackett contacts Shepard with news on that front, informing the Commander that while turian and krogan ground forces are making progress against the Reapers on Palaven, they need more support ships and the quarians are willing to talk. Hackett requests Shepard meet with the leaders of the Migrant Fleet but urges caution, as recent intel suggests suspicious activity along the geth border.

Meeting with Admirals Shala'Raan vas Tonbay, Han'Gerrel vas Neema, Daro'Xen vas Moreh and Zaal’Koris vas Qwib-Qwib at a diplomatic ship in the Far Rim, Shepard learns, much to his chagrin, that the quarians are launching another attack on the geth, with the intention of retaking their homeworld Rannoch from their AI creations. The quarians had pushed the geth back to their home system when a mysterious signal began broadcasting to all geth forces, drastically improving their combat capabilities.

Shepard concludes that the signal is Reaper tech, which must be destroyed if the quarians are to have any chance of survival. The admirals explain that the signal is being broadcast by a geth dreadnought far beyond their ability to destroy. Shepard proposes he and a squad board the vessel and disable the signal, throwing the geth into confusion and buying the quarians time to make their next move. The quarians agree and offer Shepard technical support in the form of their newest member: Shepard's old crewmate Tali’Zorah, promoted to her late father’s position based on her knowledge of the geth.

Arriving in the middle of a pitched battle between the geth and quarian fleets, Shepard and company board the dreadnought and make their way through the ship, fighting off geth crew to reach the drive core, where the signal is being broadcast. Inside the drive core is another of Shepard's old crew, Legion, who has been hardwired into the drive core to amplify the Reaper signal.

Legion explains that the quarian attack drove the geth into an alliance with the Reapers in order to save themselves. At Legion's direction, they shut down the drive core, freeing Legion from its shackles. In return it disables all shields and weapons aboard the dreadnought as a sign of good faith. Making the most of the advantage, Admiral Han’Gerrel deviates from the plan and launches a full attack on the dreadnought, hoping to destroy the crippled geth flagship, regardless of Shepard and Tali's protests that they are still inside. Shepard and his squad narrowly escaped the vessel in time.

After returning to the Normandy and condemning Gerrel's explanation of his actions, Shepard requests information from Legion. To the horror of the admirals, Legion explains that the dreadnought's destruction has only severed the Reaper signal at long range; a base on Rannoch's surface is still transmitting the signal at short range, and the geth will soon recover from the disruption. Orbital bombardments are out of the question; the geth have set up jamming towers that prevent the quarian ships from pinpointing the base.

Several sorties on Rannoch's surface are planned during the interim of determining the Reaper signal's location: the rescue of a stranded Admiral Koris, and the disabling of geth fighter squadrons attacking the liveships. Shepard begins the assault on the signal base when its location has been determined, armed with a targeting beam that can cut through the jamming signal. Legion drops in solo to disorient geth forces and provide remote technical assistance.

The plan works, but when the Normandy bombs the signal generator, it is revealed to be a Reaper destroyer. The destroyer pursues Shepard and company as they flee in a geth shuttle, while the quarians and the Normandy attempt to provide supporting fire from orbit. A chance weapons strike from the Migrant Fleet reveals a weak point in the Reaper's defenses: that the firing chamber is vulnerable when priming. Using the handheld laser guidance system and dodging the Reaper's attacks, Shepard directs the Normandy and Migrant Fleet's weapons against the Reaper, eventually severely damaging it.

Following its defeat, the badly damaged Reaper and Shepard exchange barbed words; the Reaper, recognizing Shepard from Harbinger's description, asserts that Shepard's opposition to the Reapers is pointless, that they are preserving organic life from chaos and that the cycle must continue if organics are to be saved from destruction. Shepard dismisses the Reaper's warnings and assures it that the races of the galaxy will continue to fight until a way to defeat the Reapers is found. With nothing more to be said, the Reaper "dies".

With the Reaper destroyed, the geth fleet is left disabled and vulnerable to the quarians, but Legion requests permission to upload a modified form of the Reaper code to all geth that would grant them true intelligence. Shepard was presented with another problem: the geth or the quarians? How could he choose between them? He couldn’t risk the quarian fleet, but was it right to annihilate one race or another? Then a solution was found. Having built up enough trust on both sides, Shepard declared no one would die under his watch and, with both sides owing to a multitude of factors, calls for a ceasefire and eventual peace between the races. Admiral Gerrel was stubborn though, and tried to override his orders. Losing his patience rather quickly, Shepard informed the quarians that if they didn’t stop, the geth would wipe them out. The geth didn’t want to fight them and they needed to believe that for just one second. After a pause, Han’Gerrel called off the attack. However, there was an error in the upload. Legion needed to sacrifice itself in order for the upload to complete. Much to Tali’s dismay, she understood what he had to do. Shepard watched on and bowed his head as Legion fell to the ground, lifeless. He saw a geth prime approach him and much to his surprise as well as Tali’s and Admiral Raan’s, the geth invited the quarians to return to Rannoch and live with them in peace. The conflict between the quarians and geth that has raged for three centuries was brought to an end, and the fleets of both races are acquired for the fight against the Reapers. Deep down, Shepard wondered just how fragile that alliance was. All it took was one act to trigger a war, just like how it caused the batarian hostility and eventually the Skyllian Blitz.

Fall of Thessia
"The matriarchs are growing desperate. For the first time in our history, Thessia is vulnerable. For all our intellect, we are outmatched by Reaper firepower."

- Citadel Councilor Tevos to Commander Shepard

Following the resolution of the quarian-geth conflict, Councilor Tevos requests that Shepard come speak with her on the Citadel. Though the Crucible's construction nears completion, the absence of the Catalyst still makes it useless against the Reapers. She reveals to Shepard that there is a highly classified artifact located on Thessia that may help him identify the Catalyst; however, she urged haste, as the Reapers have descended on Thessia in droves, seeking to annihilate the most advanced race in the galaxy.

En route to Thessia, Liara, who insists on coming to help defend her homeworld, explains that the artifact is housed in the Temple of Athame, a deity whose worship is nearly as old as the asari, but has fallen out of practice. Arriving on Thessia to find the asari military fighting a losing battle against Reaper forces, Shepard and the squad make their way to the temple, where a science team is purported to be waiting for them. They arrive at the temple to find a security field blocking the entrance, strangely high-security for a temple of a dead religion. When Liara deactivates it, they enter the temple and find the scientists dead, but not at Reaper hands. They search the temple which houses artifacts related to Athame's worship, including ones that look suspiciously Prothean.

While Liara explains the temple's history, Shepard comes to a realization; the artifact the asari Councilor sent them to find is a Prothean beacon hidden within the temple. Considering the temple's age, the beacon is likely the reason why the asari are technologically and scientifically ahead of the other races, and they have directly violated Council law by keeping the beacon to themselves.

The beacon is powered up by the detection of one with Prothean-like brain patterns (which Shepard received in the form of the Cipher) and once the squad fully activates it, a Prothean VI identifying itself as Vendetta appears. Establishing that it is in a post-Prothean cycle and detecting nearby Reaper forces, it attempts to shut down, but Shepard insists that it wait and provide information on the Catalyst and Crucible. Vendetta explains that the Crucible is not of Prothean origin, but is a cumulative design spanning countless galactic cycles stretching back millions of years. The Protheans themselves never used it because their efforts were sabotaged by a splinter faction who (like Cerberus in the present cycle) argued the Protheans should control the Reapers, not destroy them. By the time it was discovered the separatists were indoctrinated, it was too late; the Prothean order of battle was too fractured to coordinate an effort to activate it. Vendetta also mentions that the Protheans learned that similar patterns of evolution and dissolution occur in every galactic cycle, with each path of advancement and conflict happening differently but in fundamentally similar ways - too similar to be merely chance. Vendetta infers that the Reapers are "servants" of the pattern, not its creator, but can’t identify their true master or motive, only its intention: galactic annihilation. Before Vendetta can specify what the Catalyst is, it detects an indoctrinated presence nearby and shuts down.

The intruder is revealed to be Kai Leng who demands Shepard’s attention, pulling a drone from his coat and remarking that "Someone would like to talk with you". The drone projects a hologram of the Illusive Man, who has learnt of the Thessia beacon from the Mars Archive and mocks Liara for missing it. The Illusive Man goes on to expand on his belief and convince Shepard that controlling the Reapers is the best course of action and that the Thessia beacon contains the information to do so. Shepard asserts his conviction to destroying the Reapers and dismisses the Illusive Man's scheme, accusing him of being indoctrinated. Rebuffed, the Illusive Man orders Leng to kill Shepard and recover the data.

A vicious battle ensues, but Leng is unable to gain the upper hand. Leng calls in assistance, ordering a Cerberus gunship to destroy the temple's structural supports and the temple begins to collapse. Shepard and the squad are forced to react quickly to save themselves and by the time they recover, Leng has already acquired the data and fled aboard the gunship. They can only watch helplessly as Leng's ship escapes and more Reapers descend to complete the destruction of Thessia.

After escaping to the Normandy, Councilor Tevos contacts Shepard, though the Commander delays the meeting out of reluctance. She eagerly requests information on the Catalyst and when it will complete the Crucible, but Shepard is forced to tell her of Cerberus's interference and his failure to acquire the data. Realizing that asari civilization, maybe all civilization may now be lost, Tevos cuts communication, leaving Shepard to brood on his failure.

Retaking Omega
"I’ve amassed a fleet of merc ships. We’re going to punch through enemy lines and invade. Once we’re on Omega, it’s a ground war. That’s why I want you. I only accept the best."

- Aria T'Loak to Commander Shepard

Once rested, Shepard received a message from Aria T’Loak to meet her at the Citadel on Dock 42. He meets with one of Aria’s batarian guards, Bray, and boards an aircar with Aria to discuss her plan to retake Omega from Cerberus.

Traveling to Aria’s Fleet in the Widow system aboard a captured Cerberus cruiser in order to infiltrate the Cerberus fleet surrounding the station, Aria opens her attack with a crippling blow to the fleet’s flagship as her own fleet charges in via mass relay. The tables are soon turned, however, as General Oleg Petrovsky reveals that Omega’s defenses have been significantly upgraded by proceeding to inflict heavy damage on her fleet. The initial invasion force lands on the station in escape pods. Finally, once arriving at the control room for the defense guns that are ripping Aria’s fleet apart, Shepard locates a panel in front of a holographic map and deactivates the guns and stops them from firing, allowing the fleet to then enter Omega. Aria and Shepard, with the help of Nyreen Kandros, fight their way to Aria’s Bunker, where Aria decides that in order to get to Petrovsky’s command center in Afterlife, she needs to rally the Talons gang to her cause to supplement her ground forces, and disable the force fields that Cerberus has set up to restrict travel within the station and contain civilians.

With those tasks accomplished, the true war for Omega began as the civilians rebelled against their Cerberus occupiers. Aria and Shepard prevent Cerberus from destroying Omega by blowing up the station’s central support column, and then join in the offensive to Afterlife from the Gozu District. Nyreen, who had been leading a separate assault with her Talons, sacrifices herself to kill a group of rogue Adjutants, which Cerberus had been experimenting on during the occupation. Enraged at Nyreen’s death, Aria rushes into Afterlife and attacks Petrovsky’s final forces, including perfected Adjutants under Cerberus’s complete control. Petrovsky traps her in a stasis field, but Shepard breaks her out and defeats all the Cerberus forces in Afterlife.

Defeated, Petrovsky surrenders himself and orders his troops to stand down, but Aria punches him and then chokes him, wanting her enemy to feel how close he is to death. To everyone’s surprise, Aria spared Petrovsky’s life and hands him over to Shepard to deal with. With Omega hers to rule once more, Aria announces its liberation to the citizenry, and vows to never lose the station again. Before leaving, Aria reiterates her promise to Shepard, saying she honors her debts: her eezo supplies and a fleet are committed to the galactic war.

Leviathan
"Anything that could kill a Reaper could do a lot of collateral damage."

- Commander Shepard to EDI, about Leviathan's capabilities

At some point, an Alliance group known as Task Force Aurora, led by Dr. Garret Bryson, took interest in the Leviathan of Dis and surmised that whatever killed it might be an advantage against the Reapers in the present war. Under orders from Admiral Hackett, Aurora began investigating incidents and patterns that might lead to this Reaper-killer, the "true Leviathan of Dis". Bryson pursued several leads, including sightings of mysterious creatures around the galaxy, sites that might be frequented to gather element zero for space travel, and the activity of the Reapers as they seemingly carried out their own hunt for Leviathan. Aurora members Dr. Alex Garneau and Dr. Ann Bryson were dispatched to nexuses of these data sets, Mahavid and Namakli, to search for artifacts related to Leviathan and pick up its trail.

At Admiral Hackett's request, Commander Shepard met with Dr. Garret Bryson to assist in his investigations of myths about of the Reapers. Before he could reveal his latest discovery, however, his assistant Derek Hadley shoots him dead. Shepard subdues Hadley and calls in C-Sec. During the interrogation, EDI pores through Dr. Bryson’s research. It is implied that Hadley has been indoctrinated and he eventually falls down unconscious. EDI plays a message between Bryson and Hackett for Shepard from the computer’s logs. It appeared Shepard was the help that was requested. Upon completion of the playback, Shepard continues the scientist's work. By investigating the objects in Bryson’s lab for clues, such as audio recordings, blackout crimes, rachni activity, deposits of element zero, and Reaper activities, the study found that the files were connected to an associate of Bryson named Alex Garneau. Shepard and EDI decide to locate Garneau, mentioning that he spoke about the research for Leviathan.

On the way to the asteroid mining facility Mahavid, Shepard, Cortez and the squad discuss the details of the mission and the evidence they found while searching the lab, but also discover a small Reaper scouting party near the mining complex, signaling that if the Reapers were there then they were on the right trail. After eliminating the scouting party, the squad entered the reception room with T-GES Mineral Works employees hanging out, oblivious to the Reaper party that the Normandy team just cleared out. Shepard and team talks to the personnel at the reception desk, and after asking about Dr. Garneau, find out that the elevator is inoperable. After using a repair drone to fix the elevator, the squad moves up to the next floor and finds an undelivered message by Dr. Garneau to Dr. Bryson – which contains a working password for further clearance. Since a security terminal revealed footage of Dr. Garneau’s arrival to the facility earlier, it mentions the patient number for accessing the medical bay.

Once inside, the crew meets Dr. Garneau. After a conversation it turns out this person is being controlled by the Leviathan and it makes the thrall run away. Shepard gives chase but after the second door is sealed off, the squad finds their only way out through an access ladder going outside. The Reapers, hunting for Leviathan, sent their own forces to stop Shepard. Marauders, Ravagers and conventional Husks attack, along with a pair of Banshees. When they are dealt with, the team attempts to access the door, but power goes offline and now they have to escort a vulnerable repair drone to repair two power units. Once the repair is complete the squad proceeds further inside into the mine, where they see Dr. Garneau with his back towards the artifact and surrounded by Husks. Instead of giving Shepard a clear shot at the Husks, Garneau detonates the artifact, killing him along with the rest of the Husks.

Examining the area one of the squadmates discovers the real Dr. Garneau’s body. It turns out the man they were chasing was an imposter after all. The corpse contained encrypted data and 8 missed calls from Ann Bryson, Shepard's next link in the investigation. Some of the facility’s personnel, apparently themselves again, approach. Not only do they have no recollection of who Dr. Garneau is, they actually have no recollection of anything other than being somewhere dark and cold. When Shepard questions them about Reapers attacking the base, they don’t appear to know what a "Reaper" is. Finally, Shepard asks them what year it is. An asari miner answers 2176 – apparently the Leviathan has held the facility’s personnel as thralls for 10 years. When Shepard reveals this, the facility’s personnel appear shocked and greatly confused.

By the time of Shepard's arrival, Reaper forces have already begun assaulting Namakli in search of the Leviathans' trail. Ann Bryson is rescued, although Marauders have already begun accessing yet another Leviathan artifact found on the planet. The Leviathans once more attempt to dissuade Shepard from the search by enthralling Bryson, causing the Commander to destroy the artifact.

Left with few other options, Shepard and company resort to using the artifact in Dr. Bryson's lab, with Ann serving as the bait, in an attempt to trace Leviathan communication signals. The artifact's shielding is briefly let down, leading Ann to be briefly enthralled while EDI traces the signal. The operation is successful and Shepard eventually arrives at the source of Leviathan signals: 2181 Despoina.

There, Shepard dives to the Leviathans' lair deep under the planet's ocean and meets a Leviathan, which uses its powers to trap Shepard in their own mind. Projecting itself as Derek Hadley, a man posing as Alex Garneau, and Ann Bryson, Leviathan explains its race's history and connection to the Reapers. Initially, Leviathan refuses to help Shepard, justifying this skepticism with the fact none have defeated the Reapers before; they decide to allow the cycle to continue as planned, keeping the Commander as their servant while the Reapers harvest the galaxy as they have always done, but Shepard points out that the Reapers now know of their existence and that the Leviathans can no longer afford to remain in isolation.

Realizing that the Reapers fear Shepard for defeating Sovereign and the Collectors, other Leviathans reveal themselves. Together, they agree to aid the galaxy in the war against the Reapers, but because they still consider themselves the galaxy's apex race and not out of a desire to help "lesser species". As Shepard departs the planet, the Leviathans turn a Brute against other Husks and use their artifacts to transmit a powerful pulse that disables an attacking Reaper Capital Ship, illustrating their power.

Assassination attempt
"Spread out boys! Find me Shepard!"

- An unnamed CAT6 mercenary leader

Sometime after Cerberus’s attempted coup on the Citadel, Shepard and his crew were ordered by Admiral Hackett to go on shore leave while the Normandy is due for retrofits. Upon arriving at the Citadel, Shepard travels to Anderson’s personal apartment and is contacted by Anderson from Earth, who turns over his apartment over to Shepard, saying that he no longer needs it. After taking some time to explore the quite vast apartment, Shepard received a message from Joker requesting to meet with him at the wards

After leaving his new apartment, Shepard takes a taxi through the Citadel and into the wards. Once arriving at the sushi bar, there is a queue, but the host notices Shepard and lets him bypass the line, saying that the table is waiting where Joker waves him over. Joker comments about the ambiance and the long line outside, nodding to where an Alliance soldier in dress uniform tries to get Shepard’s attention while the host is holding them back. Shepard then changes the subject to the dry docking of the Normandy and Joker expresses reluctance in letting "shifty aerospace engineers" have their hands on the ship, to which Shepard agrees but reminds Joker that they’re on shore leave—Hackett’s orders, whether they like it nor not. After the small talk, Joker asks why Shepard invited him to the sushi bar, but Shepard replies that Joker sent the invitation. Their confusion is interrupted by the soldier outside, who finally broke through the host’s defensive line. Once she reaches the table, she introduces herself as Staff Analyst Maya Brooks of Alliance Intelligence, and proclaims that someone is trying to kill Shepard. Joker makes note of the fact that Shepard is already being targeted by multiple organizations, and that it isn’t news. Brooks restates that the group she is referring to are new people and that they are hacking Shepard’s account, communications, and are targeting Shepard personally. Shepard then tells Brooks to calm down after she tells a story about the last time she guessed at intel and tells her to start from the beginning.

At that point, several mercenaries in armor stroll into the bar, and one knocks the host unconscious. They proceed to start to fire their weapons at the ceiling, causing the restaurant patrons to panic and scatter. Shepard grabs Joker, pulls him down and flips behind the table over for cover. Brooks hides behind another table but one of the mercenaries finds and drags her away. Shepard then orders Joker to get the crew while he goes after Brooks. When Joker starts moving away, one of the mercenaries notices him and moves closer to the overturned table. Shepard grabs the enemy and uses a heavy melee to kill him. Joker complains about being used as bait but makes an escape. Shepard recovers the mercenary’s pistol, an M-11 Suppressor, and tells Brooks to hold on as he begins to fight his way through his attackers. Being outnumbered and without armor and squadmates, Shepard dives from cover to cover as much as possible and makes a beeline for Brooks, reviving her. Another mercenary targets Shepard with a Mattock assault rifle, but Brooks notices, shoves the Commander out of the way, and takes the bullet herself. Shepard tries to get to her, but the mercenary shoots at the Commander but that only ends up shattering the restaurant’s glass floor, sending Shepard on a wild ride down into the lower Ward. After several repeated attempts to stop, the Commander finally manages to fall onto a platform and stops. Clearly injured, Shepard manages to get up, recovers the M-11 Suppressor, and Brooks manages to contact the Commander. Shepard asks Brooks if she is okay and Brooks says she used medi-gel, a lot of it and is clearly a little bit tipsy. Shepard makes the comment that she probably used too much. Brooks asks if she can be of assistance, and Shepard tells her to alert C-Sec while he looks for a way out.

Moving from platform to platform, Shepard notices a landing pad. Brooks checks the area and notices it as Cision Motors. Shepard orders Brooks to get a shuttle there, but Brooks says that C-Sec had the entire area locked down and it will be difficult. Shepard orders her to keep trying. Brooks tells the Commander to stay off the comm as it is probably hacked, which she notes is probably how they found Shepard in the first place. Shepard asks who they are, Brooks replies that she doesn’t know, but they clearly don’t like Shepard. As he progresses, Ashley contacts the Commander and asks if he is okay, explaining that she is on foot but not far and that Joker filled her in. Brooks then cuts in and asks who they are as it is an unsecured channel and they are putting Shepard at risk. Ashley is confused until Shepard says that it is Brooks and orders everyone to play nice. Garrus then contacts Shepard saying he just heard, and that everyone is on the way. At the end of the bridge, locked down of course, Shepard starts the bypass, asking for a C-Sec code, but Shepard’s Spectre authorization overrides it. However, this also sets off an alarm which alerts the mercenaries to him. Ashley and Garrus both contact Shepard claiming to hear the alarm. Heavily outnumbered and outgunned, Shepard is forced to stay in cover as much as he can. Once the way has been cleared, Brooks contacts the Commander saying there is a C-Sec shuttle on the way to the lot, and that he needs to get there. Inside the door, he finds Ashley holding off two mercenaries, which are quickly dispatched. She joins Shepard to search the car lot to find the control panel to unlock the landing pad door and approach to open it, but suddenly locks. Shepard prepares to shoot the lock with a gun but Ash puts her hand on the gun and pushes it down; she calmly knocks on the window and politely asks the volus employee to open the door, which he does. She thanks him and the frightened volus tells them to leave.

Moving out the doors and onto the platform, the C-Sec shuttle arrives, but it is yet another ambush by the mercenaries who open fire with normal weapons as well as a Geth Spitfire. Shepard and Ashley duck behind cover. Fortunately, help arrives: Urdnot Wrex smashes through a window, slams into the shuttle and crashes it onto the platform; Wrex then heads inside the shuttle and cleans out the ambushers. When Shepard asks what Wrex is doing there, he claims to have been butting heads with the Council over krogan expansion. Wrex tosses Shepard the Spitfire just as another group of mercs pour in. Joker and Brooks contact the group; Joker obtained a shuttle, picked up Brooks, and is on his way to them. Once the shuttle arrives, Shepard along with Ashley and Wrex retreated to the extraction zone. Once on board, Joker pulls away.

Back at the newly acquired apartment, a conversation immediately begins about what happened. Wrex wants an explanation and Brooks says that she can’t believe Shepard survived all of that. Shepard tries to contact Bailey but Brooks and Ashley warn that doing so might make him a target. Shepard agrees and shuts down the comm link. He then asks Brooks how she got involved in all of this and explains how: she wrote a program to follow officer IDs and prevent fraud and it found someone hacking into Shepard’s file. This identity thief went through Shepard’s personal records, classified files, everything. Wrex then butts in saying when does hacking involved heavy-weapon fire. So everyone starts from somewhere and Wrex suggests that it be the pistol Shepard recovered. Wrex says that he’s never seen anything like it, and at that point, Liara walks in to examine it, and summons Glyph, who begins compiling data and disappears. Wrex wants to know about the rest of the crew, and then Joker walks in echoing the same thing and walks in with the rest of the crew.

Liara says she called in some favors to get information on the gun and it leads to a casino owner named Elijah Khan, who is suspected of using his money to smuggle weapons onto the Citadel. She continues by playing a very interesting call after the attempt on Shepard’s life between the identity thief (using an ID disguiser) and Khan. Shepard asks Liara about the mercs who attacked him; she explains that they are from a private military corporation called CAT6, which is slang for Alliance dishonorable discharges. The conversation turns to how to get Khan, and with the saferoom he has, it won’t be easy. Liara comes up with a plan, which Shepard expands on to include a small team, no gunplay, and using stealth. Glyph cuts in to say Khan is using the casino for a charity event for war refugees that evening. The topic turns to how they will get into the panic room and how to disable the camera on the door. They all go around denying for reasons until Brooks says about a class she took. Shepard then says that she is in, despite her objections. Liara mentions one last hurdle; it is a black tie event.

Shepard, Brooks and Ashley get the red carpet treatment upon arriving and they just smile and wave. Once inside, the two Spectres mingle as Brooks heads directly for the ventilation shaft. Brooks eventually calls because there is a problem: there is an alarm on the gate. Brooks gives Shepard a pair of resonance emitter lenses, provided by Liara, which allows Shepard to see and follow underground circuits. Following the blue wiring, Shepard spots a junction box at the other end of the upper level guarded by a camera. Liara uploads a program to bypass the camera, but it doesn’t last very long. Once the junction box is bypassed, Brooks gets in. After mingling a bit more, Brooks runs into another problem: there is a guard right beneath her. Shepard distracts the guard by telling him there is a red sand user in the bathroom and the guard moves to confront them, allowing Brooks to pass. She contacts Shepard again and says she has run into two problems. EDI and Liara come up with a solution, this time Shepard follows the red wiring. They lead to opposite sides of the casino. After bypassing both security devices, Brooks says that she is in the panic room and is bypassing the lock. However, she misses one of the security devices and gets caught. EDI tells Shepard that she can call the guard to tell them it is a false alarm. Once that is over, Brooks radios in that she is clear and needs Shepard to meet her. Once inside the saferoom Shepard tells Khan they are going to have a talk, except Khan can’t talk because he is dead. Brooks manages to get into the terminal, but finds a deletion order on it. Brooks starts to beat herself up but Shepard calms her and then examines the terminal for mistakes, finally finding a clue. Whoever killed Khan wiped the terminal but not the comm. Shepard activates the comm and a face appears on the screen over the mantel, distorted beyond recognition through signal degradation. Eventually, the mysterious figure says that they will take everything Shepard is and everything he owns. As the conversation cuts, Brooks says she couldn’t trace the call. Shepard orders her to remove the drives and get them back so EDI can analyze them.

Back at the apartment, Shepard orders Brooks and EDI to check the drives for anything useful. EDI and Brooks discover a communication a few days ago, and once Brooks cracks it, she opens the file. On it is a series of purchases, weapons, and big ones. Mechs are part of the included package. Glyph then interrupts to say that Shepard’s Spectre access code was just used at the Citadel Archives. Garrus explains the archives and what is contained there, very hush-hush information. Even he couldn’t get access as a member of C-Sec. As Shepard orders everyone to gear up, he finds a volus with a double pepperoni pizza. Brooks then mentions that it is sad that Shepard can’t bring everyone, but Shepard says why not? As everyone around the room voices their opinions, the volus also chimes in--apparently someone needs to pay the bill.

As the trio of X3M skycars rocket towards the archives, Shepard asks for the best way in. Brooks says that they are below the wards and suggests a direct breach for maximum surprise. Shepard agrees. As they land over the archives, Brooks mentions that it might be hard to get in. James however says that wouldn’t be a problem and pulls out a bomb. After the blast, Wrex rushes in and everyone else follows.

After breaching a room, targeting lasers come in from all over, and everyone dives for cover. CAT6 was clearly unprepared for, as everyone starts shooting. Once the room is clear, someone appears on a catwalk holding Brooks hostage. He orders everyone to drop their weapons or it won’t end well for Brooks. The mysterious identity thief finally steps out and is revealed to be a clone of Commander Shepard, created by Cerberus during the Lazarus Project in case the real Shepard needed a new arm, heart, lung, or spare parts. However, the Illusive Man abandoned the project once he had the real Shepard. The clone remained in a coma until six months ago, right when Shepard was arrested. During those months, the clone learned "how to be human" through the use of neural implants. Shepard says that he doesn’t care who his clone claims to be because the role of Commander Shepard was already filled. The clone rejects Shepard’s words, as it believes itself superior to him. The clone then proceeds to go on and eventually say that people will believe that it is the real Shepard when the clone is flying the Normandy. Shepard calls the ship to lock it down, but the comm is blocked. Instead the clone calls Traynor to prep for emergency departure, using the codes Shepard just tried to use. It then orders its goons to execute the real Shepard and his friends as it flees deeper within the archives.

Refusing to idly stand by and watch a doppelganger steal his ship, Shepard shoots the Citadel model above to bring it crashing down on the two troopers on the ground floor. Everyone springs to cover and fights their way out. Shepard orders Team Mako and Team Hammerhead to stick together and move up. Shepard eventually calls Glyph, and after persuading it, it moves off to track the clone. Shepard sees the clone moving in to flank and manages to get few shots into the clone’s side. Then Shepard runs down and covers the squad’s retreat up a ladder. Once everyone else is up, Shepard begins to radio for assistance, the rest of the team, now on the upper catwalk opens fire, ripping the enemies to shreds. Shepard then climbs the ladder, and tells everyone that they can’t be far behind and to keep the pressure up and they should get the clone. During the fight where more banter amongst the team for some funny business, Shepard asks if all of the comedians can actually start hitting something. Moving through to the next area, two CAT6 mercenaries attempt to ambush the squad. Once the fight is over, Glyph says it has found 18 previously unknown historical events. Shepard asks about the target, and Glyph says that the clone ordered it away. Shepard sends Glyph back after it. Destroying an Atlas mech, Glyph comes back to say there is a squad ahead "Razor Squad" that wishes to do bodily harm. Also, there is an elcor mating totem Glyph found to be interesting. As Teams Mako and Hammerhead flank the opposition, Glyph tries to get them to stop, only to be shot at. Once the initial group is almost dead, Razor Squad arrives with four heavies. Moving the squad around to flank them, Razor Squad is wiped out. In the next room, everything suddenly gets quiet.

Shepard tries to radio the team and the radio is once again jammed. Team Mako moves ahead to make a path. Once two CAT6 heavies are dealt with, Shepard tries to raise Mako and Brooks starts saying they are under attack, but can’t complete before being cut off. Advancing a little further Brooks confirms that the clone is indeed jamming the radios. She says the rest of the squad has gone ahead to cut the clone off, but she has been hit and needs help. The team steps in towards Brooks, but as they cross the plane, the vault’s shields activate and seal Shepard and the squad in. Shepard calls for assistance, but the clone makes an appearance. The clone says that Shepard’s companions are trapped in the iridium vaults, and then introduces its accomplice Brooks, who in fact doesn’t work for the Alliance and that "Brooks" isn’t even her name. She’s in fact ex-Cerberus, the one who put together all of the dossiers for Shepard’s suicide mission against the Collectors a year ago, but became disillusioned that Cerberus was looking to aliens for help and left the organization as the Illusive Man began his slow crawl to indoctrination. She then reveals that she is the one who orchestrated the mercenary ambush in the Wards to intercept Shepard’s Spectre code and as the one who killed Kahn at the party, while further revealing that she’s the one who woke up Shepard’s clone six months ago. Further enraged at this betrayal, Shepard threatens Brooks and the clone, but neither of them takes him seriously. The clone uses the archives to update the handprints records, which can’t be accurately cloned, and then seals Shepard and the squad into the vault. The clone then departs for the Normandy, but not before taunting Shepard with a familiar phrase: "I should go."

Despite being sealed in the vault, Shepard appeared more concerned about the way he has always said "I should go" and asks if he really sounds like that. One of the squadmates confirms it. Eventually one of the squadmates asks why Shepard isn’t more worried about their current situation, at which point Shepard calls Glyph to get them out.

Once the team managed to make it out of the archives, Joker arrives and says he has room for Shepard plus two and to hurry because the other Shepard is stealing the ship. During the ride to the docks, EDI suddenly starts to malfunction and then goes offline. She reactivates momentarily, though her visor is gone. She explains that the clone has disabled her connection to the Normandy and she cannot prevent it from taking control of the ship. Joker gets Shepard and the squad as close as possible before the Citadel’s auto targeting system brings them down. Once they arrive, CAT6 mercs pounce rather quickly. Once all enemies are eliminated, they head up the ramp and into the Normandy.

On the ramp, the squad finds Samantha Traynor furious because she was fired and dishonorably charged by the clone (whom she thinks was Shepard) for alleged conduct unbecoming. The clone kicked her off the ship with barely enough time to grab her toothbrush. Shepard convinces Traynor that the clone was not the real Shepard and the squad calms her down and explains the situation to Samantha, who she believes. They head into the airlock to get the door open, but to no avail as it is sealed. Shepard asks Traynor if there is any other way in, and she notes that there is an emergency hatch in the airlock, but that it was designed to only open from the inside. As Shepard and the squad try to figure out how to get in without tools, Traynor holds up her toothbrush to use its tiny mass effect fields to open the emergency hatch. Soon after the squad boards, the Normandy jets away from the Citadel, and the clone with the CAT6 crew is shown in the CIC. The crew has shut down a lot, including EDI, but they did register a security breach before launch. Brooks and the clone head down to the armory while ordering the crew to slow Shepard down, but the real Shepard proved too powerful for the CAT6 crew to handle. Before heading down the elevator, Shepard discovers that "somebody" dumped all his personal stuff from the cabin – ship models, space hamster, Bryson’s experiment, medals – into a big bin for disposal… further irritating Shepard.

Once inside the cargo bay, the clone emerges in a full set of N7 armor, and Shepard and the clone begin fighting. The two appeared to be evenly matched, each of them countering each other blow for blow, but Shepard gets a break as Cortez and Joker fly in a sky car in front of the Normandy, sending it on evasive maneuvers. The clone orders the CAT6 pilot to shoot them down. The shuttle then launches, leaving the hatch open. At this point, the whole ship begins wobbling from side to side as both Shepards continue to fight. Eventually Shepard tackles the clone, causing them to both tumble down the open boarding ramp and nearly falling off the edge. The clone asks what makes Shepard so special, as his squadmates arrive to pull the real Shepard up to safety. The clone looks at Brooks, who just glances and abandons it to its fate. Shepard kicks the clone off from the ramp, leading to its death.

After the Normandy is brought under control, Cortez and Joker assess the damage. Shepard has one last chat with an arrested Brooks, who is already thinking of escape. She attempts to distract the Commander with talk, but he doesn’t buy it and remains adamant on letting her rot in jail. Brooks misinterprets the intent thinking the great Commander Shepard is pleading for his life if she escapes, though Shepard retorts that it’s actually the other way around. Brooks stands down and is taken into custody. After that, the Normandy returns to dock and the team were able to continue relaxing on shore leave.

The end of Cerberus
"Cerberus is already dead. They just don’t know it yet. And when their base is nothing but a smoking crater, remember that you’re the one who helped us find them."

- Commander Shepard to Samantha Traynor

Following the disaster on Thessia, Shepard bemoans the fact that Cerberus always seems to be one step ahead and asks the crew for any intel they might have to get the jump on the organization. The Normandy ' s communication specialist Samantha Traynor mentions she had traced the route taken by Leng's shuttle as it fled Thessia as far as the Iera system, but she had lost it there, because the signal was being actively blocked. Despite the fact the only thing of note in that system is Sanctuary, a refugee camp on the planet Horizon for those fleeing the war, the Commander decides that a lead is still a lead, no matter how slim, and agrees to check it out.

Upon arriving at the facility, Shepard and his squad find signs of battle between Cerberus and Reaper forces, a surprising discovery given Cerberus’ collaboration with the Reapers. Investigating the camp, Shepard finds evidence left by former squadmate Miranda Lawson and her sister that the "refugee camp" was in truth a Cerberus laboratory run by their father Henry Lawson, working for the Illusive Man. Deeper in the facility, they discover that the refugees were being experimented on and ultimately turned into husks, in order to further Cerberus's research into indoctrination. A further bombshell is brought to light; a signal being broadcast from a tower within the facility, using Cerberus research, had allowed Cerberus the ability to control the husks created in their horrific experiments. Lawson had been working on the Illusive Man's orders to find a way to transfer this process to the Reapers themselves before the facility had come under attack, the Reapers seeking to destroy any potential weakness that could be used against them.

Fighting their way through Cerberus troopers who hadn't evacuated in time and Reaper forces left behind after the attack, Shepard and his squad makes it to the tower that has been broadcasting the signal, as well as blocking all transmissions from the planet. Here, they find Henry Lawson holding Oriana hostage and Miranda injured nearby. The Lawson patriarch tries to cut a deal with the Commander in exchange for his freedom, explaining that despite his success, the Illusive Man had merely ordered Kai Leng to retrieve the data (the assassin having already been there and gone) and leave the Lawsons to their fate.

Miranda, however, executes her father for his part in the horrific war crimes committed. After Henry has been dealt with, Miranda informs Shepard that she managed to place a tracer on Leng before his departure. Shepard and company, after shipping information about Sanctuary, learn the location of Cronos Station, the headquarters of Cerberus itself.

Shepard alerts Admiral Hackett to this discovery, and the Alliance begins making preparations for an all-out assault on the station to eliminate Cerberus and hopefully recover the Prothean VI along with any other information on the Catalyst. Hackett warns that once an assault on Cerberus is launched, the Reapers would take notice sooner or later; for all intents and purposes, the attack on Cerberus would be the first step in the campaign to retake Earth. Once military preparations are completed to Shepard's satisfaction, the assault begins.

Leading an armada to assault the station, Shepard, EDI and the squad are deployed to fight Cerberus forces in the base, while Hackett battles Cerberus’s fleet with the rest of the Alliance ships. The base is full of video logs, containing intel on EDI's past, Project Lazarus and Cerberus's new-found obsession with exploiting Reaper tech and indoctrination, and interesting tech such as prototype weaponry and pieces of the Human-Reaper salvaged from the Collector Base after its destruction. Eventually the team reaches the Illusive Man's personal office, to scour his private terminals for the location of the Prothean VI. The Illusive Man contacts Shepard again by hologram, sneering that he has already acquired the Catalyst and all he needs to control the Reapers. Again, he dismisses Shepard's claims that he is indoctrinated and assures Shepard that the idea behind Cerberus will survive any physical damage they cause to the organization itself.

The Illusive Man severs communication when EDI discovers and activates the Prothean VI. They find that Vendetta’s security protocols have been overridden and he informs the squad that the Catalyst is in fact the Citadel; in some previous cycle, the Reaper-made space station had been incorporated into the activation process of the Crucible to boost its power and coordinate its function through the mass relay system. After this revelation, Shepard realizes it then should be relatively easy to activate the Crucible, but Vendetta has more shocking news: the Illusive Man has fled to the Citadel and warned the Reapers of the plan to destroy them. As if this wasn't enough, the Reapers have already seized control over the Citadel and moved it to orbit one of their conquered planets: to be precise, Earth.

As Shepard attempts to contact Admiral Hackett to tell him this devastating news, he is cut off by the return of Kai Leng, who once again engages Shepard in a furious battle, aided by various Cerberus forces. This time, Shepard emerges victorious. After the fight between Shepard and Leng, Shepard goes to back to the Illusive Man's computer to activate the Prothean VI. Little does Shepard and his squad know, Leng survived the beating he took. After silently limping to the Commander, Leng raises his sword in an attempt to kill Shepard; the Commander senses the attack and in the nick of time disarms Leng by shattering his sword and finishes him off with an omni-blade stab, avenging Thane.

Battle for Earth
"I barely even recognize it…"

- Commander Shepard, upon seeing the devastation caused to his homeworld

Shepard alerts Hackett and Anderson to his discovery of the Catalyst's identity and location. With no alternative, Hackett and Shepard order the forces they have gathered to the Sol system with the intention of taking Earth back from the Reapers. Hackett and Anderson brief Shepard on the three-fold plan of battle: "Sword" Fleet will engage the Reapers in space, while "Hammer" ground forces will land in London. When Shepard queries why London is their landing zone, Anderson explains that the Reapers have established a teleportation beam between the city and the Citadel to transport dead and living humans to the station, presumably to be harvested. The plan is for Hammer ground forces to fight their way through the city to the beam, and get as many people as possible on board the Citadel and find a way to open the station's arms. Once this is done, Hackett will signal "Shield" Fleet, which will remain outside the Sol system protecting the Crucible, to deploy and clear a path for the Crucible to dock with the Citadel.

All forces deploy for the Sol system and a brutal space battle ensues between the fleets Shepard has gathered and the Reapers in orbit around Earth. The Normandy breaks off from the battle and descends to the planet. Shepard and several other squads having been ordered to take out Destroyer-class Reapers planet-side, fitted with anti-aircraft Hades Cannons that threaten Hammer's landing. After eliminating the destroyers, Shepard and his squad are extracted by Anderson and local resistance forces, who convey them back to their forward base. At the same time, Hammer troops begin landing en masse in preparation for the assault on the Citadel beam.

When the bulk of surviving Hammer forces have landed and deployed, Anderson briefs Shepard and the other team leaders that they must fight their way through the city to the beam, though they will need to take out another Reaper Destroyer blocking their path en route. Using Thanix missile batteries and EDI's help to overcome interference in the guidance systems from the Citadel beam, the Destroyer is brought down, but by that time, Hammer's forces have suffered heavy casualties, Reaper forces are gaining ground and to make matters worse, Hackett warns that several Reaper Capital Ships, including Harbinger, have broken away from the space battle and are descending to Earth. By the time the remnants of Hammer reach the Citadel beam’s immediate vicinity, Harbinger has already deployed to protect it.

Hammer attacks, but Harbinger annihilates them; countless soldiers are killed and Shepard's squad is severely injured. With its stealth technology, the Normandy is able to move in and carry Shepard's squad to safety without Harbinger noticing. Almost immediately after the ship’s departure however the Commander is hit by Harbinger and critically injured. Believing itself victorious, Harbinger retreats back to the space battle, not noticing Shepard managing to get back on his feet and stagger into the beam.

Upon arriving aboard the Citadel, Shepard is contacted by Anderson, who followed him up but was somehow separated. The two find themselves dumped in similar-looking tunnels; keepers prowl about and there are human corpses dumped everywhere. Staggering to what looks like a control room, Shepard and Anderson are ambushed by the Illusive Man, the skin of his face and neck rotted and riddled with Reaper tech. These "upgrades" allow him to take control of their motor functions, even forcing Shepard to shoot Anderson.

The Illusive Man again asserts the necessity of controlling the Reapers and that the Crucible will grant him that power, but it is clear to Shepard and Anderson that he is deeply indoctrinated. Despite Shepard demanding the Illusive Man to stand aside and let him stop the Reapers, the Illusive Man refuses to allow the Commander to undo his plans of controlling the Reapers. He claims that he is confident that he can control them, but when Shepard asks him if he is willing to bet humanity’s existence on it his resistance begins to falter. He desperately argues that sacrifices had to be made, but Shepard counters by saying that he had sacrificed too much. Shepard tries to convince the Illusive Man, like Saren before him, to fight his indoctrination, prompting the Illusive Man to commit suicide to escape the Reapers’ control.

With the Illusive Man dealt with, Shepard opens the arms of the Citadel and Hackett orders Shield Fleet, along with the Crucible to move in. The Crucible successfully docks with the Citadel, but nothing happens. At this point, Shepard and Anderson sit together and look at the vast blue planet beyond. Anderson tells Shepard that he is proud of him and it has been an honor to fight at his protégé’s side. After this final conversation, Anderson dies from his injuries and Shepard passes out from blood loss. While unconscious, however, Shepard is transported to another part of the Citadel. When he regains consciousness, Shepard is confronted by an entity of energy, manifesting itself in the form of the small boy Shepard saw die at the Reapers' hands when he fled Earth. The entity explains that it is the Catalyst, the creator of the Reapers and architect of their galactic purges every 50,000 years. The Catalyst explains that the purpose of such genocide is to solve the problem it was created to stop; the total annihilation of organics by the synthetic races they inevitably create. Its solution was to allow organic species to evolve to the apex of their civilization and then harvest these races, with millions of bodies and minds from each race being processed and converted into new Reapers, while the remainder of their civilizations was systematically destroyed. By doing this, the Reapers preserved the harvested races, while allowing more primitive races to have their own chances to become great, evolving on their own (though influenced along more preferable paths by mass effect technology) and they in turn would be preserved, thus ensuring that the threat of complete annihilation of organics by synthetics was averted. However, because the races of the present cycle have completed the Crucible, a feat never before achieved, the Catalyst no longer believes the cycle will work, and thus a new solution must be devised. The Catalyst offers Shepard three choices for this solution, leaving the Commander to decide the fate of the galaxy while explaining how events will play out whatever Shepard decides. The Crucible in conjunction with the Citadel, the Catalyst and the mass relays can be used in a multitude of ways: as a means to destroy the Reapers, control Reapers, or render the Reapers harvests moot by fusing organic and synthetic life together.

Shepard follows the original plan of destroying the Reapers and shoots a vital power circuit in the Catalyst chamber, causing it to explode, and using the Crucible to unleash a wave of red energy across the galaxy via the mass relay network. The energy destroys the Reapers on as well as around Earth and transmits this energy to every mass relay network through the Charon Relay before damaging before damaging the relays and the Citadel as well. Admiral Hackett notices the Crucible activate and orders the fleet to disengage and rendezvous outside of the blast zone. Joker hesitates until the last possible second, desperate to save Shepard, before reluctantly following the fleet. However, he leaves too late; the Normandy jumps to FTL speeds but is caught by the energy released from the Crucible and crash-lands in a jungle on an unidentified world. Unfortunately, the solution came at a high cost: the annihilation of all synthetics in the galaxy, leaving everyone seeking a silver lining in all of this. Admiral Hackett officially closed this incident and relates how the Reapers were defeated, saying that this victory belongs to every civilization. Even though the galaxy is devastated and the mass relays are severely damaged, Hackett is confident they can rebuild stronger than before and hopes the lessons learned would not be forgotten. He regrets that so many people will not be able to witness the future that Shepard made possible, but resolves to honor their sacrifices. Eventually, the mass relays and even the Citadel are restored, and the galaxy enters into a new era of peace.

Recovery
With the Reapers defeated, the war finally came to a pyrrhic end. Shepard was incapacitated by the explosion and, by means currently unknown, sent back to Earth’s surface where he was presumed MIA and came close to being declared dead. To the surprise of many, it was revealed that Shepard managed to survive the Crucible's blast, taking a gasping breath in a pile of rubble.

Due to the Crucible’s detonation, Shepard suffered severe injuries throughout his body: the explosion blew off his left arm and rendered many of his cybernetic implants created from the Lazarus Project inert; as a result, he was in excruciating pain, along with other chronic effects before falling into a coma. C-Sec teams recovered the bodies of Admiral Anderson and Shepard. He remained unconscious before waking up to a galaxy without Reapers, where he would be interred in the hospital to receive intense medical and psychological treatment. When he was ready to walk again, his team was waiting right outside the door, eager to reunite with the man who not only saved the galaxy, but changed their lives. He was declared a hero to all races and showered with medals and honors, becoming a legend throughout the galaxy. Hackett had another announcement as well: in a surprise and unexpected move, for Shepard’s actions and leadership throughout the Reaper invasion, he decided to circumvent standard procedures and authorized Shepard’s immediate promotion to the rank of Admiral. After Shepard was released from the hospital, Ashley walked him out. A moment of embrace was captured and spread throughout Alliance space. The pair was lavishly celebrated by the Alliance as a symbol of purity and devotion emerging from dark times.

Leaving the Alliance
"We received a report on his diagnosis in a matter of weeks. It was not good. What alarmed me as the Normandy’s chief medical officer was the increase in Shepard’s brainwave patterns, the change in his behavior, eating patterns, and unexpected bouts of severe anxiety. The nightmares just kept getting worse with each passing day. And I’m sure Shepard already knew this. The next morning, he just couldn’t handle the pressure anymore. He walked away. From everything."

- Dr. Karin Chakwas's medical report on Shepard

At some point within the next two months, Shepard received a prosthetic arm to replace the one he lost during the war. He was later present at Anderson’s funeral in London, where Kahlee Sanders was to eulogize to the Alliance’s fallen war hero. The remaining members of the allied forces who attended the funeral assembled in an area near the London burial ground while a large number of notable figures and other dignitaries were in attendance and filled the remainder of the streets. His death caused Shepard to fall into a deep depression, especially seeing how Anderson resembled a father-figure, as well as his learning that his actions destroyed EDI and the geth, and was unsure of what to do now that the war was finally over.

Due to his extensive injuries in addition to his doctors expressing worry of his mental state, Shepard was due to receive an honorable discharge but he chose not to wait and decided that he could not remain any longer. Just moments after his seeing a psychotherapist, Shepard disappeared from the public eye without a trace. No one knew for sure where he went, but those closest to him believed he went off in search of a new path.

Absent though he may have been from galactic affairs, Shepard’s story was nonetheless a thing of myth and legends in certain corners of the galaxy. His exploits in the Eden Prime War, Collector abductions and the Reaper invasion were known to the Interstellar Republic—the Citadel Council’s successor as the galaxy’s new dominant government formed during a political revolution following the signing of the Citadel-Guevara Accord that was now led by a single head of state. Alliance fighter pilot Kho Weizhang learned that Garrus knew Shepard and asked the turian to tell him a story about his friend. Garrus regaled him with the tale of Shepard’s first encounter with Saren. Members of the Revolutionary Order of Khar'shan, however, had a less-than-ideal view of the first human Spectre; Balak, leader of the surviving batarians, taught his people Shepard was an enemy who destroyed their race. Despite knowing about Shepard, the mystical elements of his life, as well as the N7 soldier in general, were seen as mythic rather than heroic.

Starting a family
Only a few months after his resignation, Shepard found happiness when he and Ashley Williams decided to get married. He asked Garrus Vakarian to attend as his best man, which the turian happily agreed to. On the day of their wedding, Shepard stared into the distance, looking up at the clear sky, thinking about Anderson and his fallen teammates who couldn’t be there for him. This concerned Ashley, but Shepard brushed it off and promised to tell her afterwards as they prepared to walk down the aisle. The two soon exchanged their vows and were declared husband and wife, surrounded by their friends and respective families.

Eventually, he and Ashley had four children—Kaidan, David, Ethan, and Carolyn.

Minister of Defense
"When T'eavius asked me to join her administration, I considered turning her down. I wanted to spend my retirement years away from the political bullshit, not be part of it. (Sighs wearily.) But that's where I am now. I don't take this Defense Minister responsibility lightly. In a way, it reminds me of my time as an Alliance soldier and a Spectre. Even if things do sound impossible, we have to try. That way our children and their children can thrive and never have to experience hardship." "Is that optimism I'm hearing from you, sir?" "Never thought I'd actually say it after all these years, but it would appear so. Imagine that."

- Shepard and his chief of staff Lauretta Harley

Nomination and confirmation
After her election in 2196, First Minister Linariley T'eavius offered the post of Defense Minister to turian General Septieus Umbotis; Umbotis declined, but recommended Shepard for the position instead. Although reluctant, Shepard eventually agreed and became one of the few members of the T'eavius Administration to work and socialize with Linariley.

His nomination was approved by members of the Senate Armed Forces Committee on a 18–2 vote, and officially confirmed by the entire Galactic Senate.

Social issues
A controversy arose when Shepard addressed social issues that engaged the widest public interest; at his direction, the Ministry of Defense allowed the krogan to serve in the Republic military and the quarians to join in technical research divisions, overriding a request by the Salarian Union to continue to exempt them from certain positions.

Great Galactic War
Not long after being sworn into office, a conflict developed between the Interstellar Republic and the sudden emergence of the Yahg Empire one month later, a move which caught many off-guard. Despite Shepard's warnings about the dangers of the now spacefaring yahg, the Cabinet of Ministers led by elcor Minister of State Patrozi opposed taking military action in favor of diplomacy, viewing the yahg as a poorly equipped and ill-funded species. Several like-minded ministers also did not believe that the Yahg Empire posed a serious threat and limited naval forces to sector patrol in Citadel space in order to avoid provoking the yahg.

In response, Shepard threatened to sue his colleagues for allegedly "overstepping their constitutional authority and undermining the efforts made by the Ministry of Defense to effectively provide military assistance to deter war and maintaining the capability of preserving galactic security" in the Supreme Court; to prevent a costly, legal battle, Linariley rescinded Patrozi and the other cabinet ministers' order.

He worked to provide more manpower to meet the demands of both the Cold War in the Attican Traverse and across Republic-controlled space. Shepard also worked to coordinate a multi-species efforts with the Systems Alliance and Turian Hiarchy, as well as with the Krogan Empire and rogue STG strike teams.

Following an increase in yahg military aggressive in the Traverse, war was officially declared on September 6, 2197. Shepard and Republic High Command sought ways to aid its fleet and ground troops. In the debate over what to do about the yahg, Shepard opposed a cease–fire on the grounds that it would make the Republic look weak in yahg's eyes, and risk the Terminus Systems taking advantage of the crisis. In addition, Shepard argued that the Republic had a moral obligation to honor its commitment to maintaining galactic security. When the Asari Republics suggested diplomatic overtures to the Yahg Empire, Shepard was opposed, arguing that it was impossible to negotiate with them. In addition, when some in the Senate favored confronting Parnack, Shepard argued to stress the importance of containing the yahg.

In 2198, however, the Yahg Empire and Republic Defense Fleet engaged in a titanic battle at the Citadel. Although it ended in a Republic victory, the battle resulted in the deaths of First Minister Linariley T’eavius and most of the Cabinet of Ministers, resulting in Shepard becoming the new First Minister of the Republic as defined by the succession rules. However, Shepard was nowhere to be seen among the wreckage of Citadel Tower, though his wife expressed confidence that he was still alive.

Succession
"T'eavius is dead. Skipper... you're the new First Minister."

- Ashley Williams to John Shepard

Shepard was later found alive near Docking Bay D24 helping a small group of C-Sec officers driving off the last of the yahg presence, though he was unaware of his new status. Upon being informed of the situation by his wife, Shepard is initially very reluctant to assume the office so quickly, stating he is no politician and prefers to fight in battle. Ultimately, he is persuaded by Ashley and their children after realizing that his refusal could jeopardize not only the fate of the Citadel, but the rest of the galaxy as well.

In the days following the disaster, Shepard takes charge of the war effort against the Yahg Empire. In a conversation with Primarch Adrien Victus, he expresses the irony of being in the same position as Victus was twelve years earlier. Shepard gave his first public address to the Senate in a speech broadcast live throughout Republic space stating:


 * "No words could more or less honor First Minister T'eavius's memory than continuing to fight for those less fortunate than us. Rather than give into despair, we must instead come together as one, side-by-side and our heads held high. No matter what comes our way, there is no obstacle too great for the people of this galaxy to overcome; we've proven that in the past when the Reapers invaded, and have the capacity to do so once more against the villainous Yahg Empire."

The wave of grief following the attack gave enormous momentum to Shepard's promise to win the war.

Upon the Great Galactic War's conclusion with the Republic emerging victorious, Shepard was formally sworn in as the 4th First Minister by turian Supreme Court Associate Justice Aptius Octavitumus. During the inauguration, he was accompanied by his wife Ashley, their sons Kaidan, David and Ethan, their daughter Carolyn, and a host of friends and guests.

Legacy
"We are travelers, constantly moving forward and looking back. Alone and as one. We have no choice but to try. For our insatiable curiosity. For our fear of what should happen if we don't. You are that explorer now. We will say goodbye, and you will look back one last time and know that wherever you go, we will be with you. This is Commander Shepard, signing off."

- Audio log of John Shepard

Upon defeating the Reapers and ending the cycle of extinction forever, Shepard became a legendary figure known as "The Shepard" and one of the most influential figures in the galaxy, attaining a status as one of the finest soldiers in history. His legacy was marked by great harmony and prosperity, and by a great renewal of cooperation between the various species of the galaxy, fostered by his vigorous rebuilding campaign that eventually led to a new era. His accomplishments would be remembered for decades. Within the annals of the N7 program, basic training would see all recruits in its program learning the Adrenaline Dash, which was based on Shepard’s signature ability during the Collector Crisis.

At some point between 300-400 years in the future, an old man known as the Stargazer tells the story of "The Shepard" to a young boy. This implies that Shepard’s heroic exploits ultimately led to him becoming regarded as a demi-god, a near-mythological status among humans. Shepard is mentioned again in 2819 by Alec Ryder and the "Benefactor" as being the reason for accelerating the Andromeda Initiative's launch to the Andromeda Galaxy ahead of schedule to escape the Reaper threat.

List of characters killed by Shepard
The following is a list of characters Commander Shepard has killed: Mass Effect Mass Effect 2 Mass Effect 3
 * Matriarch Benezia – Shepard was forced to kill Matriarch Benezia after she was overpowered by indoctrination after briefly resisting it.
 * Ventralis – Shot by Shepard after Captain Ventralis confessed to following Benezia's orders, and that he sent Shepard and the squad to the hot labs in the hope that the rachni would kill them.
 * Kaidan Alenko (Caused) – Knowing he could save both Kaidan and Ashley Williams from the geth or nuclear explosion, Shepard was left no choice but to leave Kaidan behind to defend the bombsite.
 * Saren Arterius
 * Cathka
 * Morinth (Caused)
 * Donovan Hock (Caused)
 * Collector General (Caused)
 * Tela Vasir
 * Dr. Amanda Kenson
 * Dr. Eva Coré
 * Donnel Udina
 * Henry Lawson (Caused)
 * Shepard's Clone
 * Kai Leng
 * Illusive Man (Caused)
 * Harbinger
 * EDI (Caused)

Personality and traits
"People are messy, awkward, sometimes selfish and cruel. But they’re trying, and I’m going to make sure they have a chance."

- John Shepard to Liara T'Soni

Shepard is seen as an incorruptible pillar of goodwill, kindness, compassion, and strength; a paragon of virtue who feels that his own happiness and wishes always take backseat to keeping people prosperous, even at his own suffering. Though constantly making hard decisions, he normally tries his best to solve a problem with the least amount of death and conflict, whether it is rational to try or not. Above all else, Shepard is tenacious, calm, patient, deliberate, and intuitive. He appeared to be wise beyond his years and was said to be a very nice person (until given a reason not to be). He was, in many ways, the exact opposite of Saren Arterius: Shepard got things done right, not fast. He puts the needs of others, including his crew, ahead of himself and shows to deeply care for his crew, saying that they are all a big family.

David Anderson remarked that Shepard was a shrewd person, and was not a man who would do something unless it was of the utmost necessity, if there was no other way, or not without a good reason. He possessed great knowledge of the Reapers, whereas others would simply dismiss them as a myth. Regardless of the perils of imminent death and personal endangerment, Shepard was known for his indomitable spirit, drive, determination, and fierce tenacity and will not quit until he accomplishes the task at hand, even when the entire universe is in peril, getting destroyed around him or begins to weigh heavy on him.

Despite his unquestionably selfless and compassionate nature, if pushed, he will not hesitate to either threaten or gun down anyone stupid enough to get in his way. He apparently does not tolerate treachery, xenophobia, terrorism or greed lightly, as he resolved that he would do anything and everything in his power to protect the peace he worked so hard to attain. Shepard did, however, experience both emotional and psychological trauma: Staff Lieutenant Kaidan Alenko’s death on Virmire shook Shepard to his core, but he never wavered in his resolve to bring down Saren and Sovereign. When his friend Thane Krios died of a mortal wound he received from Cerberus assassin Kai Leng during Donnel Udina’s coup attempt, he vowed vengeance against the man and looked into Anderson’s reports about him. He noted during the Reaper War that it took a lot to get him worked up, but when he did, he would go on a merciless rampage against his enemies. The mass slaughter of refugees at the hands of Henry Lawson in order to study how indoctrination worked was enough to drive even the benevolent Shepard into a bloodlust rage. After the failed mission on Thessia and briefly succumbing to his anger, he showed Cerberus troops no mercy and ruthlessly killed any who stood in his way and expressed a feeling of exhilaration that he had never felt upon killing Kai Leng at Cronos Station.

Since the start of the Reaper invasion, Shepard made it his mission to stop the Reapers and that he must shoulder its responsibility alone, forcing to constantly show an air of calm, confidence and no fears or worries. He continued to do so until the fall of Thessia, even though he continued to insist that he was fine, Joker pointed out that according to EDI’s armor metabolic scans this line of thought, coupled with pushing himself too hard, will only increase the amount of stress he was already under. Over time, Shepard’s demeanor begun to fade, slowly beginning to crack under the pressure of deciding the fate of the entire galaxy and showed a great deal of worry, fear, exhaustion, loneliness and questioned whether he could actually pull it off. Afterwards, Shepard acknowledged his shortcomings in his attempts to do things himself, and allowed others to help him instead of shouldering burdens himself. Due to this, he demonstrates his leadership throughout the course of the war as he successfully forms a krogan-turian alliance, cured the genophage, negotiates a truce between the geth and quarians, as well as uniting the galaxy while ultimately leading the Citadel Allied Forces to victory against the Reapers and Cerberus personally.

In the aftermath of the Reaper invasion, Shepard's optimistic nature was shattered and he became embittered as well as grief-ridden; cold and emotionally withdrawn, he gained a cynical outlook on life, thinking that the galaxy itself was a cruel place. The death of his mentor and father-figure Admiral David Anderson seemed to finally break Shepard as he doesn't know what to do anymore after so much loss. His new apparent lack of empathy became increasingly stronger to the point where he doesn’t care about his well-being, concerning his friends with Jack remarking with a slightly remorseful tone that Shepard has "lost his mind" and Garrus Vakarian believed the fight was ultimately kicked out of him. As noted by Admiral Steven Hakett, rage and the feeling of powerlessness can turn a good man like him into a cruel one. This was the case as Shepard took offense at anyone speaking ill of Anderson and would "respond" without hesitation, not caring if he ended up killing them, as shown when he almost beat Ka’hairal Balak to death and mercilessly broke ex-Cerberus agent Sonya Weston’s neck when they provoked him. Garrus, Tali, Liara and Ashley all became concerned about that, as they thought once Shepard reaches a breaking point, he could snap.

After marrying Ashley and having three sons and a daughter with her, Shepard began to slowly regain a bit of his former self and allows himself to relax in comfort, although that doesn’t mean he doesn’t get angry depending on his mood. Shepard does (in some degree) retain a sense of his humanity, however. When several Council-aligned diplomats attempted to convince Shepard that they wished to make peace with him, he openly chastised and degraded them, which further strained his relationship with the Citadel Councilors but after learning they were actually serious, Shepard took a moment to calm himself down and personally noted that they would have to prove it if they wish to earn his trust again.

At some point following the formation of the Interstellar Republic, Shepard continues to be treated with an immense amount of hero worship and as a public figure whose opinions are taken seriously within the new government. However, Shepard seemingly appears to have withdrawn from public life in order to care for his family. At some point within this period of time, he returned to the public eye when he was appointed to serve in the T’eavius administration as the Republic's Minister of Defense and knows full well of the mistakes of the past, often advising his colleagues not to repeat them.

Appearance
Shepard was a tall, fair-skinned athletic man toned in muscle who stands at 6 feet 2 inches tall with blue eyes and almost black hair that was shaved upon joining the military and keeps a clean shaven and sometimes stubble appearance. According to Liara T'Soni, he is considered to be very handsome by most women—human and aliens alike.

In 2183, Shepard wore a charcoal grey N7 armor with a red and white stripe on the right forearm as well as bearing the N7 logo on the left side of his chest, symbolizing the blood he must sacrifice to save the galaxy. During his off-duty hours, Shepard would usually wear a sleeveless tank top (white, blue or black) and a pair of jeans as well as his military dogtags with his service number on them around his neck.

Two years later, Shepard’s outfit underwent modification after his death and resurrection. The N7 armor donned a more blackish color with more durable attachments on his shoulders, arms, chest, legs and waist. Shepard was occasionally seen wearing a black and white Cerberus officer’s uniform with golden cufflinks around his wrist and a yellow Cerberus insignia while onboard the Normandy SR-2. During his infiltration into Donovan Hock’s estate, Shepard briefly sported a black suit with a white collar and a white dress shirt underneath. When he was brought back to life via the Lazarus Project, Shepard had glowing red scars along his jawline and brow, but after undergoing surgery his scars were completely healed and faded. His body also underwent cybernetic modifications, considerably augmenting his physical parameters and increasing his lifespan. After destroying the Collector Base and quitting Cerberus, Shepard simply wore a crewman’s outfit.

By the time the Reaper War begun in 2186, Shepard’s traditional N7 armor remained the same with the exception of additional items to the omni-tool on his right arm. During his testimony at an Alliance tribunal, Shepard wore a battle dress uniform, which was worn to shreds and covered in blood when the Reapers invaded Earth. In addition, he wore an Alliance officer’s dress blues with three grey stripes on both of his shoulders with golden cufflinks around his wrist and regained his dogtags when he was recommissioned, and continued to wear it throughout the war. While off-duty, Shepard was seen wearing an N7 leather jacket with the N7 logo, red stripes on both of his shoulders, a white t-shirt, navy blue jeans and black shoes. He also claimed to possess an N7 hoodie, but has not publicly been seen wearing one. Sometime after the Crucible’s activation, Shepard loses his left arm and most of his armor was obliterated – bearing several burns and scars across his body. He soon acquired an advanced cybernetic forearm to replace his severed one.

When he and Ashley married, Shepard was wearing a black tuxedo, white collared dress shirt, black tie and black dress shoes. Many years later, Shepard grew his graying hair slightly longer and has it brushed back even as a few bangs hung over the right side of his face. He also wears a black collared uniform-style jacket donning the N7 insignia with red stripes, along with navy blue pants and dark shoes.

Summary of service
Vocational Codes: N7, A7, D3, R2

Dates of rank

 * 2172: Serviceman 3rd Class
 * 2173: Serviceman 1st Class
 * 2174: Service Chief
 * 2175: Operations Chief
 * 2176: Staff Lieutenant
 * 2178: Lieutenant Commander
 * 2180: Commander
 * 2187: Admiral

Awards and decorations
The following is a list of awards and honors awarded to John Shepard. These include awards and decorations of the Systems Alliance, civilian awards, interspecies honors, and knighthoods. Medals and ribbons=


 * Star of Terra
 * Medal of Honor
 * Navy Cross
 * Navy Distinguished Service Medal
 * Silver Star
 * Alliance Legion of Merit
 * Navy and Marine Corps Medal
 * Bronze Star
 * Navy and Marine Corps Commendation Medal
 * Navy and Marine Corps Achievement Medal
 * Purple Heart
 * Meritorious Service Medal
 * Navy Combat Action Ribbon
 * Navy and Marine Corps Expeditionary Medal
 * Navy and Marine Corps Good Conduct Medal
 * Galactic Defense Service Medal
 * Armed Forces Service Medal
 * Outstanding Volunteer Service Medal
 * Luna Service Medal

Badges= Interspecies honors=
 * Armed Forces Expeditionary Medal
 * Skyllian Blitz Campaign Medal
 * Space Service Deployment Ribbon
 * Basic Military Training Honor Graduation Ribbon
 * Long Service Medal
 * Distinguished Service Medal
 * Medal of Heroism
 * Honorarium of Corporate Service
 * Distinguished Combat Medal
 * Medal of Valor
 * Medal of Exploration
 * Colonial Savior Medal
 * Navy Expert Rifleman Medal
 * Navy Rifle Marksmanship Ribbon (with Sharpshooter Device)
 * Navy Expert Pistol Shot Medal
 * Navy Pistol Marksmanship Ribbon (with Sharpshooter Device)
 * N1 Acceptance Award
 * Distinguished Galactic Shooter Badge
 * Council Legion of Merit
 * Spectre Inductee
 * Palaven Platinum Cross

Assignments

 * 2172: Systems Alliance enlisted service
 * 2176: Participant, Skyllian Blitz (awarded Star of Terra for extraordinary bravery in defense of Elysium)
 * 2177: Student, Interplanetary Combatives Academy, Rio de Janeiro, Brazil, Earth
 * 2178: Participant, Raid on Torfan
 * 2179: N6 designation
 * 2181: N7 designation
 * 2181: Crewman, SSV Tokyo, Fifth Fleet
 * 2183: Executive Officer; later Commanding Officer, SSV Normandy SR-1
 * 2183: Spectre, Office of Special Tactics and Reconnaissance, Citadel Council
 * 2183: Participant, Battle of the Citadel
 * 2183: Missing in action
 * 2184: Killed in action (presumed)
 * 2186: Reinstated into active service
 * 2186: Commanding Officer, SSV Normandy SR-2
 * 2187: Retired from active service

Skills and abilities
"It is clear why the Reapers perceive you as a threat. Your victories are more than a product of chance."

- Leviathan to Commander Shepard

Class= Powers= Abilities= Weaknesses=
 * Soldier: Soldiers are pure combat specialists: no one is tougher or more suited to taking down enemies with barrages of gunfire. Soldiers have thorough weapons training and can use all special ammo types as well as grenades. High-level operatives are outfitted with ocular synaptic processors that allow them to focus on targets with lethal accuracy.
 * Adrenaline Burst: If necessary, Shepard can "reset" the restrains (which is located in the brain) on his body's muscles if he overexerts himself which temporarily allows him to use his abilities again at a faster rate.
 * Adrenaline Rush: Shepard's signature technique, he awakened this power in both his eyes at a very young age. For a brief moment, it slows down time around him and predict movements while his endorphins block out pain and trauma with minimal drain on his stamina. In addition, according to Shepard's perspective, whenever this technique is active, his enemies appear as if they're standing still.
 * Ammo Modification: Shepard can augment the ammunition in his firearms to deliver punishment.
 * Armor-Piercing Ammo: Tears through armored targets.
 * Cryo Ammo: Freezes enemies, turning them to ice.
 * Disruptor Ammo: Tears through kinetic shields and synthetic enemies.
 * Incendiary Ammo: Tears through armored enemies, setting them on fire.
 * Shredder Ammo: Tears through organic enemies
 * Warp Ammo: Tears through armor and shields.
 * Biotics: Upon receiving secondary exposure to element zero at 14 and fitted with L3 implants at 17, Shepard can manipulate dark energy and create mass effect fields through the use of electrical impulses from the brain.
 * Barrier: Creates a forcefield to protect oneself from damage.
 * Charge: Increase the mass of one's body and charges at enemies with great force.
 * Dark Channel: Plagues enemies with mass effect fields, priming them for biotic combos.
 * Dominate: Attacks the mind of the opponent, leaving them under Shepard's control for a short time.
 * Flare: Focuses and expends huge amounts of biotic energy to release a powerful energy blast.
 * Lash: Grabs enemies with a whip-like mass effect field.
 * Lift: Suspends enemies in the air for a short time.
 * Nova: Punches the ground with biotic energy with great force.
 * Pull: Pulls enemies off the ground and into the air for a short time.
 * Reave: Absorbs the life-force of the opponent.
 * Slam: Lifts enemies in the air them slams them with great force.
 * Shockwave: Releases a wave of mass effect fields.
 * Singularity: Traps enemies in a singularity field.
 * Stasis: Traps enemies with a stasis field, leaving them vulnerable to attack for a short time.
 * Throw: Hurls enemies in the air with a mass effect field.
 * Warp: Warps enemy defenses with a mass effect field.
 * Carnage: Shepard fires a vicious blast, tearing enemies apart and deal major collateral damage to those nearby.
 * Cluster Grenade: Grabbing from his kit, Shepard can throw multiple biotic grenades at once and send his enemies flying.
 * Concusive Shot: Shepard can fire a single high-powered round from any of his firearms that damages a target and can either stun for a few seconds or release high-energy explosive charges with an impact radius large enough to knock down multiple enemies at short or long range.
 * Frag Grenade: Grabbing from his kit, Shepard can throw an explosive, shrapnel-packed frag grenade to rip his enemies apart.
 * Flashbang Grenade: Grabbing from his kit, Shepard can throw a flashbang grenade to stun enemies for a short time.
 * Fortification: By altering the chemistry of the prime ingredients of the armor, Shepard can fortify the strength of his shields as well as increase melee damage for a short time.
 * Inferno Grenade: Grabbing from his kit, Shepard can throw a grenade augmented with incendiary munitions to cluster-bomb a small area and lit his opponents aflame.
 * Lift Grenade: Throws a grenade that suspends enemies in the air.
 * Proximity Mine: Grabbing from his kit, Shepard sets a ground mine to blow up enemies when they step within range.
 * Sticky Grenade: Grabbing from his kit, Shepard can throw and stick a grenade to his enemies and watch as the resulting explosion tear apart the target and deal shrapnel damage to other enemies caught in the blast.
 * Above peak human physical and mental conditioning: As a highly skilled and experienced soldier, Shepard is in top physical condition (from intense workouts at the Interplanetary Combatives Academy and his numerous mission assignments), and while possessing an extraordinary amount of stamina and a high degree of pain tolerance, his muscular and athletic physique make Shepard immensely physically powerful by normal human standards. A match for seemingly any opponent, it was noted by Dr. Liara T’Soni and Lieutenant James Vega that Shepard is easily one of the Alliance’s most gifted soldiers that ever existed.
 * Above peak human agility: Shepard has demonstrated superb nimbleness and agility, quickly moving across walls with almost ape-like acrobatics and gymnastics (which furthers the suspicions of others that Shepard is inhuman and supernatural), and even dodging gunfire from a krogan’s shotgun, with the aggressive reptilian biped barely getting a glimpse of Shepard, as the first human Spectre’s speed and agility made him appear as blurs of motion (on par with Kai Leng himself), enhancing the inhuman and supernatural illusion further. His seemingly inhuman mobility allows him to move away from the sight of others. Also, Shepard could jump several feet into the air over a large container while slamming a man into it. Shepard even managed to jump away from several immensely powerful Destroyer-class Reaper beam weapons.
 * Above peak human durability: Shepard was also exceptionally durable by human standards (further enhanced by his cybernetic implants), as he could not be slowed down or fazed by falling from a ceiling, allowing him to land on his feet and quickly attack opponents. This also allowed Shepard to be unfazed when being shot at or physically assaulted.
 * Above peak human endurance: His endurance was far beyond the average Alliance soldier (further enhanced by his cybernetic implants) and is able to keep performing actions for extended periods of time without succumbing to exhaustion, but may still have certain limitations on how much stress his body can take. Shepard can sustain himself at peak capacity for several days as he has shown himself capable of fighting during the Skyllian Blitz for over 24 hours despite facing overwhelming enemy forces. His lung capacity is at peak human level, enabling him to hold breath for 6 minutes under water.
 * Above peak human strength: By properly using physical forces, momentum and leverage, as well as his knowledge of anatomical weaknesses and strength based exercises, Shepard is able to seemingly simulate high-level superhuman strength. Hence, Shepard is capable of easily lifting and hurling humanoid opponents over his head, knocking them out with a single blow, throwing people into walls hard enough to break through them, punching people hard enough to send them headfirst into the floor and their head through the floorboards, effortlessly smashing through wooden walls and sending people flying through the air several feet. Due to numerous cybernetic enhancements to his body under the Lazarus Project, this upgrades allows Shepard to hit even harder, inflicting more damage with his punches as seen during his fight with the yahg Shadow Broker, a pre-spaceflight species who are more than twice a krogan’s size and strength. Also, Shepard could jump several feet into the air over a large container while slamming a man into it.
 * Expert marksman: Shepard is a highly skilled marksman, utilizing firearms and heavy weapons with a high degree of accuracy, notably using ricocheting a pistol shot to wound Tela Vasir without harming a hostage, and shooting off a LOKI Mech’s head from a great distance.
 * Expert martial artist: Shepard has been fighting since he was a boy, as such, his killing intent is ever-present and his survival instincts grants him an intense concentration that further increases his strength and speed. This makes Shepard an expert tactician on and off the battlefield.
 * Hand-to-hand combatant: Due to his harsh childhood and with 15 years of military experience, Shepard is an extremely skilled hand-to-hand combatant. His fighting style also incorporates the prior use of physical forces, momentum and leverage, as well as combining his N7 training with street fight techniques, executing it all at very high speeds. With his tremendous combat skills, Shepard effortlessly brought down a Reaperized husk of Saren Arterius (despite being quite exhausted after fighting off Saren’s combined geth and krogan army right before), has brought down the Collectors, can overpower even physically stronger opponents, like the Shadow Broker, and brought down quite a few batarian shocktroopers during the Skyllian Blitz. In fact, Shepard is the one who defeated most of Cerberus’ elite agents—including Kai Leng. Under Shepard’s tutelage, his apprentice James Vega would become a highly skilled N7 operative in his own right.
 * Genius-level intellect: Despite having little formal education, Shepard is very intelligent, to the point that he has successfully gone toe-to-toe with the extremely dangerous adversaries during his military career. However, Shepard is notably not quite as intelligent as the Illusive Man, with the latter thereby successfully outsmarting and manipulating Shepard into working with him against the Collectors by turning any political support and allies from him as well as putting the most sympathetic individuals on his crew, with Shepard never suspecting it and figuring it out only after the Illusive Man knowingly sent him into a trap aboard the Collector Cruiser.
 * Diplomacy: Shepard is regarded for having a keen, diplomatic mind as he is able to know how to pick and choose his words carefully and negotiate between opposing parties (i.e., politicians, military leaders, etc.) to garner the results he wants.
 * Leadership: Shepard has a gift for being a great military leader, highly charismatic and very skilled with experience in combat. As such, he obtained countless loyal followers. Miranda Lawson draws attention to this, claiming that Shepard has "that fire that makes someone willing to follow you into hell itself." Urdnot Wrex added that it was this leadership that made Shepard the first to accomplish what no one else could: uniting a galaxy. Shepard's charisma, drive, and martial skill have undoubtably saved the galaxy at least once over from the alien menace and continue to be a guiding light for the entire galaxy to rally behind. In addition to impressive personal ability in numerous aspects of soldiering, Shepard possesses an enviable ability to rally others to the cause, whether those others are recalcitrant governments or a fractious crew of alien fighters. The exploits of Shepard's motley crew against the Reapers and their servants are the stuff of legends, and most of those who follow Shepard would be heroes in their own right, were they not overshadowed by the more famous human.
 * Multilingualism: He is able to speak a variety of languages besides his native Basic, such as speaking fluent French, Spanish, Dutch, Italian, German, and Swedish; however, as a result of the Cipher he received on Feros, he is able to understand the Prothean language.
 * Indomitable willpower: His mental fortitude is noteworthy, having displayed great determination and strength of will, which make him an extremely formidable opponent. His willpower proved strong enough to withstand the effects of a Prothean beacon and more resilient to an asari mind-meld as well as a brief resistance to a Leviathan's enthrallment. Years prior to the Reaper invasion, even when Sovereign declaring Shepard's attempts to stop the Reapers futile and demonstrating its staggering amount of power, Shepard showed no signs of fear and countered Sovereign's threat with one of his own. Later, when leading the allied forces against the Reaper fleet's full might, Shepard refused to back down from the seemingly hopeless battle against the seemingly unstoppable dreadnoughts, persistently attempting to expose them to the Crucible, ultimately succeeding, thereby greatly contributing to the Reapers' defeat.
 * Intimidation: As a veteran of the Skyllian Blitz, his various accomplishments have earned him much renown, and praise from his comrades and he holds a position of great influence. In battle, Shepard was a force to be reckoned with and gained praise from allies and foes alike as seen during his first fight against Saren Arterius on Virmire, with the turian commenting that Shepard was not fighting with even half his strength. The Illusive Man, founder and leader of Cerberus, also stated that Shepard never ceased to amaze him. Most alien species are very aware of Shepard’s capabilities, and, upon meeting him on the battlefield, either feared for their safety or grew excited at the idea of fighting. Harbinger acknowledged Shepard as a threat and tried to kill him out of fear that he would someday interfere with its plans. This concern was later confirmed by the Leviathans when they realized that the Reapers feared Shepard for defeating Sovereign and the Collectors.
 * Keen eyesight: His most distinguished talent is the Adrenaline Rush ability, which grants him a heightened sense of perception.
 * Potential: A natural-born genius, Shepard was noted by his drill instructors that his progress hardly required any help. According to those who knew Shepard personally, he was hailed as a very talented prodigy – a rare genius that appeared only once in a generation, making a strong impression on the Alliance High Command by graduating top of his class from the Interplanetary Combatives Academy at twenty-two years old and rose quickly through the military ranks in a short amount of time. David Anderson, one of the Alliance’s most famous war heroes, took a special interest in Shepard and took him on as his student and even admitted that Shepard was far stronger than he was at the time when he himself received the N7 designation. Two years after the end of the Reaper War, Shepard’s improved prowess allowed him to defeat Terminus System’s warlord Ezramon, and he received many visitors from different parts of the galaxy. He became so powerful that Urdnot Wrex remarked that Shepard’s very presence and name alone were enough to incite terror to his enemies on the battlefield and could easily handle both Rajanni and her clones simultaneously despite his battle senses dulling. Later on, after six months of intense training in isolation, Shepard’s strength and speed increased dramatically, with it being stated that he could effortlessly dodge bullets and either incapacitate or kill an opponent with a single blow if chosen to fight seriously, though he admitted that he found it difficult to adjust to his new abilities. According to Javik, Shepard’s newfound capabilities have an "overwhelming power that the cycle has never seen before." As such, Shepard is widely regarded as one of the strongest individuals in the galaxy.
 * Human vulnerabilities: Shepard's greatest weakness is that he is quite vulnerable to the physical attacks of stronger and more powerful opponents. However, he usually compensates for this quite well with his combat skills, his nigh-superhuman physical condition, and brilliant tactical intellect.
 * Subtle psychological manipulation: Shepard, despite his intellect and combat experience, can ultimately still be outsmarted and manipulated himself, though the Illusive Man is notably the only one known to have ever successfully done so, due to him being one of the few individuals superior to Shepard in intellect. The Illusive Man did so by turning away any political support and allies from Shepard by leaking reports of him working with Cerberus during the Collector crisis as well as putting the most sympathetic individuals on Shepard's crew. Shepard initially never suspected this, and is tricked into joining forces with the pro-human terrorist organization to defeat the Collectors―with only the deception revealed on board the disabled Collector cruiser and the Illusive Man's suggestion of using a radiation pulse to wipe out all living Collectors at their main base of operations and leave the base intact despite witnessing every captive human being liquefied.

Equipment

 * Combat knife
 * Assault Rifles
 * M-8 Avenger
 * M-15 Vindicator
 * M-76 Revenant
 * M-96 Mattock
 * Collector Assault Rifle
 * Geth Pulse Rifle
 * Flashbang grenades
 * Medi-gel
 * Omni-tool
 * Omni-gel
 * Omni-blade
 * Geth Combat Software
 * Sync Laser

Ashley Williams
"There are regs against this, you know. Are you ready to deal with the consequences? I spent my whole life fighting to get what I want. To get it done, I had to bury a lot of things. During that whole time, not even once did I feel like I was worth what I was fighting for. You make me feel good enough."

- Ashley Williams to John Shepard

Ashley Williams is the granddaughter of disgraced General Williams and a fellow soldier in the Systems Alliance. The two first met during the geth attack on Eden Prime, moments after her entire squad Unit 212 was wiped out. She was an NCO who held the rank of Gunnery Chief, while Shepard was an officer with the rank of Commander. When she was reassigned to the SSV Normandy SR-1 and began serving alongside Shepard, Ashley developed at first a growing admiration and came to like him.

Being bitterly discriminated against by her superior officers based on her family surname, Shepard was perhaps one of the very few to treat her with kindness and rebuke any social stigma directed towards her, something Ash greatly appreciated. Overtime, the more she opened up to him, her admiration gradually blossomed into love. A small way in which she showed Shepard her affection for him was through the playful nickname which she constantly called him—"Skipper." After the mission on Virmire against Saren Arterius resulted in the death of Lieutenant Kaidan Alenko, their bond was briefly shaken to their core; in her grief, Ash blamed Shepard for saving her life instead of Alenko's, but was silenced when Shepard called her out for trying to be a martyr on a mission to redeem her grandfather's honor. Both apologized to each other afterwards.

When the Council locked down the Normandy 's systems, Ash convinced Shepard not to give in and they nearly kissed before being interrupted by Joker. En route to Ilos, she visits Shepard in his quarters, saying that, after a long career of being sidelined by the Alliance, he helps her to feel "good enough." The two officially shared their first kiss and spent the night together, making the most of what short time of rest during the chaos and uncertainty of stopping Saren as well as delaying the Reapers' inevitable return. She continued to tease Shepard; claiming to have something important to tell him, but if he wants to hear it, he'll have to survive Ilos and come back to her first. When Shepard was killed by the Collectors one month after the Battle of the Citadel, Ashley was shocked and heartbroken by his death, and attended his closed casket funeral.

Two years later, while attempting to move on with her life, Ash was reunited with her former lover on Horizon when Shepard was brought back to life by Cerberus to fight the Collectors. They share a brief emotional reunion before things escalated into a shouting match; though she was glad to be reunited with Shepard, she voices her disapproval of the idea of Shepard working for Cerberus, feeling that the he might feel indebted to the pro-human organization for being resurrected. Ashley then leaves and tells Shepard to be careful. Despite this, it is revealed that a picture of Ashley is displayed in Shepard's quarters aboard the Normandy SR-2, showing that Shepard still cares for her. Before venturing beyond the Omega-4 Relay to destroy the Collector Base, Shepard gazes at her picture for several moments and smiles at it. Sometime after the mission, realizing she made a terrible mistake, Ashley sent an email to Shepard apologizing for her behavior. She reaffirms her feelings towards Shepard, telling him to "just stay alive out there...Skipper. I can't lose you a second time." To her relief, Shepard survived the suicide mission and forgave Ashley and the two planned on trying to rekindle their relationship when Shepard's mission was over.

Unfortunately, they never got a chance one year later as Shepard ended up being arrested for destroying the Bahak system resulting in the deaths of over 300,000 batarians. When Shepard didn't fight the charges, Ashley began to wonder if maybe Cerberus really had changed him. This led to them not seeing each other again until they were forced to work together to find important data on Mars when the Reapers returned to launch their full-scale invasion. During that mission, Shepard insisted that he was still the same person Ashley fell in love with and that he wanted her to be with him. Those moments and all the times Shepard visited Ashley while she was in the hospital helped to slowly remove the lingering doubts she still had. She even said to Shepard that if she had anything to say about it, she wanted to come back to the Normandy after she became a Spectre.

Later on, Ashley sends Shepard an email asking to meet her on the Presidium. She tells him how her dad would have liked Shepard, before apologizing for all that has happened between them and asks if they are "going somewhere". When Shepard reciprocates, they kissed and rekindle their romance. Ash was also present to help foil an assassination attempt on Shepard's life by a clone created by Cerberus during shore leave. When real opportunities for R&R arise, Ashley meets with Shepard at the Silver Coast Casino's upper bar and challenges him to a drinking contest to prove who is a "real Spectre" and who's just pretending to be one. Shepard matches her shot-for-shot, but the two have their evening interrupted by a batarian and a vorcha, with the former persistently poking Shepard and proclaiming their dislike for "Alliance types". Shepard quips "rain check" to Ash, and the two "Alliance types" proceed to beat up the aggressors. Next morning after throwing a big party, Shepard and Ashley awake in his bed and kiss each other good morning before rising.

Just before the assault on the Cerberus headquarters, Ashley visits Shepard in his quarters and tries to comfort him about all the people they’ve lost. She expresses how she felt lost herself and that it broke her heart when Shepard was dead. He expresses how he couldn't have made it this far without her, saying that he knows a good thing when he sees it. Ash attempts to back away, only for Shepard to gently cup her chin and, at long last, finally admits his love for her. Touched by his confession, they embraced and made love.

During the final assault on Earth, they spoke to each other for what seemed to be the last time, loitering near a couple of soldiers and a structure housing the London FOB’s holographic communications terminal. Restless when Shepard inquires how she’s holding up, she asks back if they have a chance, and he assures her there’s always hope as it got them so far. Ashley praised Shepard as the reason all of them got to where they are now, and Shepard answers that she and other people like her picked him up when he stumbled, Ash quips back that "hero-man" saved her almost as many times as she saved him. She feels it’s been a thousand years since Eden Prime, finding it hard to figure out how they got to their current situation. Ash was always a survivor, and Shepard compliments her as such, though she doesn’t really believe it until Shepard adds that she’s also a Spectre and a fine soldier. He then recites from one of Tennyson’s poems "The Charge of the Light Brigade", a reference to how poetry has been used to convey their feelings throughout their relationship. Fearful, Ashley grabs Shepard and tells him she doesn’t want him to go and that she loves him. He gently replies that he loves her too and says "let’s get it done, and go home". In a breaking voice, Ashley responds "aye aye Captain." However, she is badly wounded by Harbinger during the final push towards the Conduit and evacuated to the Normandy. When Shepard was prepared to destroy the Reapers, the last thing he sees will be a flashback of Ashley looking at him and warmly smiling before being engulfed in the Crucible's explosion.

Film

 * 2186: Blasto 7: Blasto Goes to War! (as himself)

Publications

 * Leviathan Codex (co-authored with Dr. Ann Bryson)
 * The Normandy: A Study in Heroism and Official History of the Reapers, Volume One

Behind the scenes
John Shepard is portrayed by Dutch model Mark Vanderloo in the Mass Effect trilogy.

Quotes

 * -|Spoken by Shepard=

Mass Effect

 * (to Joker, about Nihlus’s presence) "They don’t send Spectres on shakedown runs."
 * "I don’t like soldiers dying under my command."
 * (to Ashley) "You’re a good soldier, Williams. You belong on the Normandy."
 * (to Garrus, about his methods) "What were you thinking? You could’ve hit the hostage!"
 * (about the Citadel) "The Council represents more races than I thought. No wonder they’re careful with newcomers."
 * (to Navigator Pressly) "No matter how strong you are, allies make you stronger."
 * (to Liara) "All children rebel against their parents. It’s a natural part of growing up."
 * "If getting the job done means endangering innocent people, then no. We get the job done right, not fast."
 * (to Finch) "My gang days are over, Finch. Get out of my way."
 * "Humans are aggressive. We think fast, we move fast. Wars have started because of our need for constant progress."
 * (to Urdnot Wrex, about the krogan in Saren’s facility) "Wrex, these krogan are not your people! They’re slaves of Saren! Tools! Is that what you want for them?"
 * (to Sovereign) "You’re not even alive. Not really. You’re just a machine, and machines can be broken!"
 * (about leaving Kaidan to die) "There is no right choice for something like that. I just hope I never have to go through it again."
 * (to Ambassador Udina when he grounds the Normandy) "Nobody stabs me in the back, Udina! NOBODY!"
 * (urging Saren to resist Sovereign’s indoctrination) "Some part of you must still realize this is wrong! You can fight this!"
 * (endorsing Captain Anderson to the human Council position) "We need someone with the courage to stand up for what he believes in. Someone like Captain Anderson."
 * "Sovereign was only a vanguard. The Reaper fleet is still coming. Hundreds of ships, maybe thousands. And I'm going to find a way to stop them."

Mass Effect 2

 * (to Jacob) "I wiped out my fair share of Cerberus projects when I was a Spectre. Back then, they were trying to kill me. Why the change of heart?"
 * "Did you say two years? I’ve been gone that long?"
 * (to the Illusive Man) "You might be the reason I’m still alive, but that doesn’t mean I trust you."
 * "The Alliance lost eight cruisers. Cairo, Cape Town, Emden, Jakarta, Madrid, Seoul, Shenyang, Warsaw. And yes, I remember them all. Everyone in the Fifth Fleet is a hero. The Alliance owes them medals. The Council owes them a lot more than that. And so do you."
 * (to Jack) "I’m offering to be your friend. You don’t want to be my enemy."
 * (to Grunt) "My name is Shepard and I don’t take threats likely. I suggest you relax."
 * (to Ashley) "I’m sorry, Ash, but I was clinically dead. It took two years to bring me back. So much time has passed. You’ve moved on. I don’t want to reopen old wounds."
 * (to Nassanna) "You kill people because you think they’re beneath you, that they’re in your way. I kill people when they leave me no choice."
 * (about the Illusive Man’s deception) "He tries something like that again and the Collectors will be the least of his problems."
 * "The Collectors are just servants of our real enemy. And we’ve all seen what their masters are capable of. They built the mass relays and the Citadel. Who’s to say they can’t build a space station surrounded by black holes? No wonder nobody’s ever returned from a trip through the Omega-4 mass relay."
 * (about the Human-Reaper) "This thing is an abomination."
 * (to the Illusive Man) "I’m not looking for your approval. Harbinger is coming and he won’t be alone. Humanity needs a leader who’s looking out for them. From now on, I’m doing things MY way, whether you agree or not."
 * (to Liara) "People are messy, awkward, sometimes selfish and cruel. But they’re trying, and I’m going to make sure they have a chance."
 * (to Harbinger) "Maybe you’re right, maybe we can’t win this. But we’ll fight you regardless. Just like we did Sovereign. Just like I am doing now. However insignificant we might be, we will fight, we will sacrifice, and we will find a way! That’s what humans do."

Mass Effect 3

 * (to the Alliance Defense Committee, when they consult him for advice on how to deal with the Reapers) "Stop them? This isn’t about strategy or tactics. This is about survival. The Reapers are more advanced than we are. More powerful. More intelligent. They don’t fear us and they’ll never take pity on us."
 * (to Liara) "You haven’t seen what the Reapers did to Earth. How is one weapon supposed to stop them?"
 * (about the Council’s inaction) "They’re in for a rude awakening. Every species will fall, one by one, if they don’t work with us."
 * (to Dalatrass Linron, fed up with the salarian negotiation stance) "How long do you think you’ll last alone against the Reapers? Because if you don’t help, that’s how it’ll end up."
 * (to Mordin) "Formulating a cure that works for every krogan sounds like a tall order. Can you do it?"
 * (about Kai Leng) "I don't care who he is. Next time we meet, he dies."
 * (ordering the Migrant Fleet to stand down) "The geth are about to return to to full strength. If you keep attacking, they’ll wipe you out. Your entire history is you trying to kill the geth. You forced them to rebel! You forced them to ally with the Reapers! […] The geth don’t want to fight you! If you can believe that for just one minute, this war will be over! You have a choice. Please. Keelah se’lai."
 * (to Leviathan) "You’re responsible for this. Every race that’s ever been destroyed is because of you. And now the Reapers will destroy you, too—unless you start fighting. Even if you survive the battle today, the Reapers won’t stop—ever. Release me, and we have a chance to end this once and for all."
 * (to General Oleg Petrovsky) "It's a shame you're on the Illusive Man's side, Petrovsky."
 * (threatening Brooks and his clone) "Fair warning: nobody who’s ever betrayed us has ever survived. You two may think you’re clever. And yeah, you were, just a bit, but clever doesn’t beat a bullet. And yeah, maybe I am trapped in here, but don’t get comfortable. Because that bull’s-eye on your back is getting bigger by the second."
 * "I’m still me. I doubt I’d been able to turn against Cerberus otherwise. I don’t remember anything. Maybe they really just fixed me, or maybe I’m just a high-tech VI that thinks it’s Commander Shepard. But I don’t know. I…"
 * (killing Kai Leng) "That was for Thane, you son of a bitch!"
 * (to the Illusive Man) "Because of you, humanity is already undone."
 * (witnessing Admiral Anderson's death) "Anderson? Stay with me. We’re almost through this. Anderson? Anderson!?"
 * (to the Catalyst) "The defining characteristic of organic life is that we think for ourselves. Make our own choices. You take that away, and we might as well be machines, just like you."

Mass Effect: A Hero's Legacy
Admiral Hackett:
 * "That’s the problem with politicians. They make big promises, but in the end, they’re won’t actually do anything. Just look at what happened with Saren, the Collectors… and especially, the Reapers. (Chuckles bitterly.) That’ll give you an idea of what the typical politician is good at."
 * "Anderson was like a father to me. And I know he’d do whatever it took to make this work, and since he’s not here for me to ask for help… well, I guess it’s my responsibility to make sure this doesn’t all go to hell."
 * (to Ambassador Osoba) "I know what I said. My trust was misplaced."
 * (to Baron Ezramon) "Don’t even think about it, Baron. If you want to continue blaming me for your parent’s deaths so you can sleep better at night, fine. But know this: you even so much as attack me like that again or if I so much as catch you anywhere near my family, I will end your pitiful existence without hesitation."
 * (to Balak) "After all you’ve done to these people, you don’t deserve to live."
 * "You’ll regret ever trying to pick a fight with me. You’re going straight to hell!"
 * (his thoughts on fatherhood) "For a while I was broken. I lost my friends, loved ones, people I fought alongside with since the beginning… I had to pull myself up and keep going. To be able to move forward with my life. Though I still have nightmares, I don’t have them as often anymore. The doctor says that it will take time before they are gone completely, but some days it feels like I’m not making any progress… that I will never be over the memories of those that I lost. When I’m at my worst, I remember what is dear to me. What I fought for while aboard the Normandy. And in those moments I remember that I am not alone. And I will never be alone again…"
 * -|Spoken about Shepard=
 * "When you went up against Sovereign, there was no good reason to believe you'd win. But your crew didn't seem to care. They went along anyway. Your trip through the Omega-4 relay? That was a suicide mission if there ever was one. Yet there your crew was, standing beside you, proud to serve. Why? Because they believed in you, their leader. That's what I need now. Where we're taking them is likely to get pretty hairy, and I know you're the one who will get us to the other side."

David Anderson:
 * "Sure, I can talk about Commander Shepard. Big topic. There's been a lot written about the Commander, but most of it isn't true. People are quick to judge. They don't know the whole story. I don't even know the whole story. But I know the man. Worked with him, fought with him. Trust him with my life. Shepard's had some rough patches. Who of us hasn't. He's been forced to fight a lot of battles alone. God only knows how he got out of some of that. Makes your head spin.


 * Thing is, you never heard a complaint. Never once got "No, sir. I can't do that." He never hesitated. Few people know what Shepard's been through. I'd like to think I come pretty close. And I worry sometimes he forgets: there's a whole bunch of people who lose sleep over him getting back home. Maybe it doesn't need to be said. Maybe we're too dumb to say it.


 * Soldiers like the Commander are rare. Men like Shepard... even more rare."

Squadmates:
 * "The Illusive Man ordered my creation years ago. Jeff was the one who allowed me to think for myself. But only now do I feel alive. That is your influence." —EDI


 * -|Conversations=
 * EDI: "I was running scenarios in my head to analyze Jeff's behavior. I believe he has a strong affectionate attachment to me, but he has not stated it to anyone yet. Shepard, you have firsthand sexual experience. How do you know when someone is romantically invested?"
 * Shepard: "They'll usually show signs they can't stop thinking about you. You know: asking you out, giving you presents, maybe playing music..."
 * EDI: "I lack material wants other than hardware and software upgrades, and my core programming does not assign values to music. Perhaps we could discuss how to provoke Jeff into an emotional commitment."
 * Shepard: "That's not how to think of it. It's got to be natural. You need chemistry."
 * EDI: "I see. There are a number of pharmaceuticals I could inject to simulate the desired emotional state..."
 * Shepard: "No, I mean relax and do something you both like. Something simple. For example, you both like humor."
 * EDI: "Correct. I will see if there are comedic entertainment shows being presented on the Citadel. Scanning... Do you think he will like "The Man Who Hung Himself"? It appears to be about an amorous plastic surgeon."
 * Shepard: "EDI, the important thing is to have a good time, wherever you go. And if you're having fun, he will too."
 * EDI: "Then the outcome is an unknown quantity, but you're saying I should attempt it anyway."
 * Shepard: "Nobody ever fell in love without being a little bit brave..."


 * Shepard: "You've forgotten everything you stood for. Cerberus was supposed to be humanity's sword, not a dagger in our back!"
 * Illusive Man: "Poetic, but as usual, you miss the point. The world is more grey than you care to admit."
 * Shepard: "With the Prothean data, I can end this conflict once and for all. You're either with me or you're against me. There's nothing grey about that."

Trivia

 * He is named after Alan Bartlett Shepard, Jr., the second person and the first American in space (May 5, 1961). He later commanded the Apollo 14 mission in 1971 and became the fifth person to walk on the moon.
 * Shepard’s birthday (April 11) is the same day that Apollo 13 (an American attempted manned moon landing that almost ended in disaster) was launched (April 11, 1970).
 * He seems to speak with a hint of a Canadian dialect.
 * When Shepard is inducted as a Spectre, according to Admiral Hackett, Shepard is, technically, still part of the Alliance military (though Captain Anderson claims otherwise). Therefore, Shepard should still be referred to as a Commander, even though Shepard is outside of the Alliance military’s chain of command and answers directly to the Council.
 * Military ranks can, in some situations, be deferred in favor of civilian ranks. Considering the nature and authority of Spectres, it is likely that this is considered to supersede any military rank.
 * He is a terrible dancer.
 * Shepard had a cameo role in the movie Blasto 7: Blasto Goes to War!, in which he played himself.
 * He is a good cook.
 * To keep the exact nature of Shepard’s return quiet in 2185, it is often stated that Shepard almost died, which is not really truthful. He would later joke with Jack that he is "technically undead".
 * Shepard is apparently a fan of the Seattle Sorcerers biotiball team.
 * The Shepard Memorial Plaza on Elysium and Shepard Memorial Scholarship on Earth are all named after him.
 * He once shared a kiss with Aria T’Loak.