A rising star in the cadre of the new Terran Federation Marine Corps recruits, Jonathan Shepard came from a family with strong military traditions, both his parents were ship captains. In his early childhood, he was raised on the Terran Federation top secret naval base at Sanctuary, although he has also experienced life on various other ships and stations, including the Citadel due to the nature of Shepards family's jobs as Naval officers, transferring posts to different locations, never permantly in one place.
In their parents' footsteps, he and his sister Johanna enlisted for Federal Service at the age of 18, although both initially stated the Navy as their main preferences, due to Jane's lower skill set and lack of compulsion, only John was admitted for Federal Service as a Marine Corps recruit for the Navy while Jane ends up as a K-9 Corps recruit in the Army. He would go on become one of the most decorated Terran war heroes throughout his tenure as a Federal Marine trooper in the First and Second Batarian Wars.