Facility Zero is a secret, hidden base operated by Chronos on the frozen ice planet of Crilles. Facility Zero houses the Megaton Program, whose sole purpose is to supply The Master with an army of R-61 Battletroopers, also known as "Supermen" or "Pro-Humans".
The head operative of Project Megaton, Dr. Beckett Jarvis, also holds command over the facility. When Commander Shepard first investigates the facility, Jarvis claims that the base is the main headquarters of Maestro Pharmaceuticals, which is - in truth - a cloak company founded by Jarvis to hide Project Megaton.
After Jarvis is killed by Shepard, they can decide to destroy the base and the Battletroopers (Paragon), or they can use the base and the Battletroopers to fight the Reapers (Renegade).