After the First Contact War Cerberus was created. Cerberus only hires humans. They were lead by the Illusive Man. When Comamnder Shepard was killed by a Reaper the IIlusive man had him revived so, he could work for the IIlusive man. Over time after Commander Shepard destoryed the collector base he rsigned from aiding Cerberus. Even though Cerberus did do good they became more and morel ike villians over time. Cerberus began transforming their human operatives. Cerberus even took over Omega but, Commander Shepard and Aria T'Loak took Omega back.
They attack the alliance and the Citadel killing a Council member but, Shepard stopped them from defeating the council memebrs. Commander Shepard helped defeat these foes in a number of missions. Shepard lost a battle at Thessia.During the attack of Cerberus base Kia Leng was kileld by Comamnder Shepard. After the final battle against the Reapers the Illusive Man held a gun at Commader Shepard and Admiral Anderson but, Comamnder Shepard defeats the Admiral by either shooting him or convincing the Illusive Man orb y convicing him he had been indoctrinated causing the Illusive man to shoot himself.