The movie begins aboard the experimental SSV Normandy, commanded by Captain Anderson and his executive officer, Commander Shepard. The Normandy is being sent to the human colony world of Eden Prime to recover an unearthed Prothean beacon. To assist in recovering the beacon, the Citadel Council, the main government for most of the galaxy, have sent one of their top agents, a turian "Spectre", named Nihlus.

Nihlus, Shepard, and a small team discover that the Eden Prime colony is under attack by alien synthetic life-forms known as the geth, led by a rogue turian Spectre named Saren Arterius, who kills Nihlus. After the battle ends, Shepard locates the beacon and receives a vision of biological creatures being slaughtered by machines.