Commander Anderson sent Shepard and his friend,Kaiden to the human colony of Eden Prime to recover an unearthed Prothean beacon. They repel an attack by the geth,rescuing Ashley,but losing Nihlus Kryik,member of the turian spectre,who was killed by his former mentor,Saren Arterius before the beacon was activated. Shepard reaches the beacon and receives a vision of war and death. The SSV Normandy and its crew are summoned by Ambassador Donnel Udina to the Citadel Station,but Shepard is unable to convince the Citadel Council of Saren's treason without solid evidence.

Shepard rescues Tali'Zorah,the Quarian Mechanic,who possesses a recording of a conversation between Saren and asari Matriach Benezia about an artifact called the "Conduit". Shepard goes on the planet,Therum,along with Kaiden,Ashley,Tali,Urdnot Wrex,a krogan mercenary,and a turian,Garrus Vakarian,to retrieve Benezia's daughter,Liara T'Soni,who joins his Squad. They soon confronted Benezia,who reveals that She and Saren are being indoctrinated by Sovereign,a flagship of Saren. After they manage to defeat her,Benezia tells them that Sovereign must be stop. Saren appears and kills her.

Back at the Ship,Ashley joins Shepard in the shower and begun making love. Assisting the Salarians in destroying the base by planting a bomb,Shepard is confronted by Sovereign,who reveals to be the Reaper. Kaiden and Ashley are confronted by Saren,who fatally wounds Kaiden. Shepard manages to overpower him and they quickly escape. The Reapers are beginning to invade.

Shepard's Squad manage to stop them. Shepard fought Saren,killing him. As Reinforcements finish off the Reapers,Sovereign reanimates and possesses Saren's corpse to attack Shepard. Garrus fires a Rocket Launcher,destroying Saren's corpse. The SSV Normandy and the Alliance fleet finally destroys Sovereign. The Council tells Anderson and Udina that the Reaper threat can still continues. Shepard tells Ashley that he will end the Reaper threat.