Chasing after Kai Leng and the Illusive Man, Shepard finds Sanctuary, a world devoted to taking refugees. However, it’s a false front. Cerberus is using the humans for experiments on Reaper indoctrination, turning people into husks. Miranda’s father leads the research. He does discover a way to reverse engineer the process, so that he thinks he can command Reapers. Kai Leng escapes with the data and returns to the Illusive Man. Because Miranda’s planted a tracker on Leng, he leads Shepard and the Alliance to Cerberus’ doorstep.
Admiral Hackett goes for a final check-in: once the fleet makes a move on the Illusive Man, the Reapers will become aware. The Crucible is ready except for the Catalyst. Everyone hopes that the Illusive Man knows what it is and how to implement it. Otherwise, humanity battles Reapers over Earth as, probably, a last stand. Shepard gives the go-ahead.
Immediately, we’re back in the molasses realm, chasing that Boy.
Shepard in armor watches as Boy runs into the arms of Shepard in casual wear. They all gaze at each other. Shepard awakens in bed wearing her underwear. (This is the point where Shepard becomes intimate with anyone she romanced. I just couldn’t work up the energy to care, although I’ve pursued all the options in the past.)
And then we’re on Cronos Station, the Illusive Man’s base.
It’s a straightforward fight into the center to recover the Prothean VI. Along the way we see the giant skeleton Reaper from the Collector base. Apparently the Illusive Man retrieved it. It’s just hanging there in tatters.
We also watch some video logs. The first is about the beginning of the Lazarus Project. Shepard was brain dead, although the helmet kept her head intact when the rest of her body was spaced. In all of the conversations with the Illusive Man nothing unexpected is revealed. He really did bring the authentic Shepard back. No tinkering happened during her rebuilding. The same cannot be said for the Illusive Man. The final log, which takes place after the Sanctuary events, indicates that he has Reaper tech implanted. The doctor worries about indoctrination, but the Illusive Man insists.
After a boss battle with Kai Leng we talk to the VI. The Catalyst, it reveals, is the Citadel. It and the Crucible must be near each other to work. However, the Citadel has been already moved. The Illusive Man, who no longer wants to destroy the Reapers but to control them, has notified the Reapers of the plan. They’ve parked the Citadel over Earth, making the odds of beating them impossibly long.