User blog comment:Kaloneous/Mass Effect 3 Ending DLC Denied and PAX/@comment-2250460-20120322233255/@comment-1683278-20120322234533

That doesn't explain why Shepard wakes up in the ending surrounded by concrete, and it doesn't explain why Joker was flying the Normandy away from the battle. If you think about what Bioware has put in the game (the kid that only Shepard seems to notice, the dream sequences, the very obscure plot holes in the ending fight), Indoctrination seems more logical than anything else.