Prologue
"You brought me back to lead the fight against the Reapers. If you can keep up with it, good. Otherwise I'll win this without you." And indeed, he did.
The Illusive Man proved more ready to the fight than Shepard thought possible. In the weeks after the attack on the Collector Base, Cerberus completed numerous successful operations against the remaining Collector forces, leaving the galaxy some room to breathe. But it was just a matter of time, and they both knew it. The Reapers were about to invade in mass, and no matter the scale of their efforts, cleansing the galaxy of Collectors and Husks was as useful as teaching a varren how to drive the Normandy.
But it felt like doing the right thing, and it sure was better than just sitting around waiting for the inevitable.
And then the Arrival came. Harbinger and the Alpha relay were still vivid in Shepard's mind. The sight of a whole solar system blasted away from the Universe. What he did had been harsh, brutal, and morally ambiguous. Was sacrificing all [insert number here] really justified? He felt so, and that's why, after destroying the relay, Shepard decided to join Cerberus indefinitely, because he knew that they would do anything to stop the Reapers, no matter the cost. And that's when things started to go to hell.
His mission on Noveria had been a failure, the Normandy had also been lost, and the Alliance captured him, bringing him all the way back to Earth, where he was to be judged for his actions in the Bahaka system.