Two years have passed since Commander Shepard defeated the Collectors. His old team has split up, and he is back to working for the Systems Alliance, the organisation representing the interests of humanity in the galaxy.
Shepard is on Earth when the initial Reaper forces arrive and begin their assault on humanity. Leaving Admiral Anderson behind to co-ordinate the resistance, he leaves with Major Kaidan Alenko and Lt. James Vega to unite the races of the galaxy into an army capable of liberating Earth and defeating the Reapers.
On Mars, Shepard finds Liara T'soni, a former squadmate, scientist and information broker, along with the blueprints of The Crucible, a weapon which could potentially wipe out the entire Reaper army in a single shot. However, he still needs to assemble an army, and this overarching mission takes up the majority of the storyline.
Shortly after the Mars mission, the Normandy's AI, EDI, occupies the body of a robotic scientist found on Mars and becomes a squadmate. If the From Ashes DLC is installed, Shepard travels to Eden Prime, where he finds the last surviving Prothean, Javik, who has been in stasis for several millenia.
After rescuing the Turian Primarch from his Reaper-devastated homeworld, in the process finding and recruiting his old squadmate Garrus Vakarian, Shepard manages to unite two formerly hostile races, the Turians and the Krogan. At this point, he can either doom the Krogan to extinction by leaving the deadly genophage intact, or cure the genophage and give the Krogan a future.
It is revealed that the human ambassador to the Citadel Council, Donnel Udina, has been working with Cerberus, a human supremacist terrorist organisation and one of the main antagonists of the game. Cerberus attacks the Citadel and kidnaps the other councillors. However, Shepard manages to rescue the councillors, and Udina is killed.
In the Perseus Veil, Shepard must resolve a conflict between the Geth, a synthetic species, and the Quarians, their creators. Here, he meets and recruits Tali'Zorah nar Rayya. The Quarians wish to return to their homeworld, which has been overrun by Geth, triggering a war between the two races. Shepard must decide whether to allow the Geth to upgrade and destroy the Quarians, leave the Geth to die, or, if he has prepared well, form a new alliance between the races.
Shepard is directed to the homeworld of the Asari, Thessia, in order to locate the Catalyst, the component without which the Crucible cannot function. After coming under heavy Reaper bombardment, Shepard finds a virtual intelligence belonging to the Protheans, a long-extinct race, which claims to know how to finish the Crucible. However, the data is stolen by Kai-Leng, a Cerberus agent.
The Final Battle
The Alliance manages to locate Cerberus headquarters, and Shepard finds the virtual intelligence once more. It reveals that the Citadel itself is the Catalyst for the Crucible. The Illusive Man, the leader of Cerberus, has escaped, but Shepard manages to defeat and kill Kai-Leng.
The Illusive Man, revealed to be indoctrinated by the Reapers, has moved the Citadel into Earth orbit, to keep it from being used as the Catalyst. The forces that Shepard has assembled are all ordered to move to liberate Earth immediately. Shepard and a small team fight their way to the tractor beam which will take them up to the Citadel, and narrowingly avoiding death at the hands of Harbinger, the leader of the Reapers, Shepard staggers into the beam.
On the Citadel, Shepard finds both Admiral David Anderson and The Illusive Man, and each of them advises him in turn on what to do. Anderson states that the Reapers must be destroyed, and The Illusive Man maintains that it is possible to control them and use them for the benefit of humanity. Both end up dead, and Shepard proceeds alone to the final decision.
Shepard finds the Catalyst here, not actually the Citadel itself but an artificial intelligence running within it. The Catalyst explains that the Reaper cycle was created to save organic races from being destroyed by the synthetics they create. The organics “ascend” as Reapers rather than being wiped out. This is the first cycle in which the organic races of the galaxy have united the Catalyst and the Crucible, and thus the Catalyst accepts that the Reaper solution is no longer viable. Here, Shepard is offered a choice. He can use the Crucible to wipe out all synthetic life in the galaxy, including both the Reapers and the Geth. This is coded red. He can attempt to control the Reapers, as the Illusive Man did. This is coded blue. The final option, coded green, is to merge synthetic and organic life into one new type of life, ending the conflict and destroying the Reapers.
The Fate of the Galaxy
The Mass Relays, used to travel long distances across the galaxy, are all destroyed. The Reaper threat is ended. The Normandy, Shepard’s ship, crashes on a planet, and its crew steps out. Shepard is presumed to be dead, although he could potentially be alive if the “red” option is chosen. The game ends with a grandfather recounting this tale to his grandson on an unknown world, whilst they gaze at the stars.
Free downloadable content has been announced to expand and clarify the ending, without changing it. This content has yet to be released at the time of writing.