Commander Anderson sent Shepard & 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 & receives a vision of war & death.
The SSV Normandy & its crew are summoned by Ambassador Donnel udina to the Citadel Station,but Shepard is unable to convince the Citadel Council of Saran's treason without solid evidence. Shepard rescues Tali'Zorah,the Quarian Mechanic,who possesses a recording of a conversation between Saren & Matriarch Benezia about an artifact called the "Conduit". Shepard goes on the planet,Therum,along with Kaiden,Ashley,Tali,Urdnot Wrex,a krogan mercenary,& a Turian,Garry's Vakarian,to retrieve Benezia's daughter,Liara T'Soni,who joins the squad. They soon confronted Benezia,who reveals that She & Saren are being indoctrinated by Sovereign,a flagship of Saren. After they manage to defeat her,Benezia tells them that Sovereign must be stop before she is killed by Saren.
Shepard & Ashley are having a romantic moment. Later,Shepard & his squad begun planting bombs in the base. They are confronted by Sovereign,who reveals to be the Reaper. Saren attacks the Squad,killing Kaiden. Shepard manage to overpowers & kills him before the Squad escapes. The Reapers are beginning to invade.
As the Squad manage to stop them,Shepard is attacked by Sovereign,reanimated & possesses Saran's corpse. Garrus fires the Rocket Launcher,destroying Saren's corpse. The SSV Normandy & the Alliance fleet finally destroys Sovereign. The Council tells Anderson & Udina that the Reaper threat can still continue. Shepard tells Ashley that he will end the Reaper threat.
