***SPOILERS*** IF YOU HAVENT FINISHED THE GAME YET
http://www.youtube.com/watch?v=ythY_GkEBck
This theory seems very plausible imo. After all when you do choose destruction you notice sheppard waking up. And the rubble arround him looks more like earth than the citadel.
Everything gets weird after you get shot by harbinger.
1. Your pistol has infinite ammo.
2. After you get shot by harbinger and stand up you can see trees and bushes that you couldnt see before. EXACTLY the same as those in your dreams chasing the kid.
3. Captain anderson did not notice the kid at the start of the game. And he suddenly vanishes. Indoctrination illusion ?
4. When the kid goes on board of the ship. Nobody pays attention to him. Nobody tries to help him get up on the shuttle.
5. When you face captain anderson and the illusive man. You should notice blurry dark shadows surrounding the enviroment.
6. Also you should notice that they both never talk to eachother. BUt ONLY TO YOU. Captain anderson litterly looks at you when he says. "LISTEN TO YOURSELF YOU ARE INDOCTRINATED".
7. Every renegade option seems to be what i would call a paragon option and every paragond option seems to be a renegade option. Why add renegade options in the game at this point in the first place ? Its all a trap preventing you from doing the right thing.
8. After captain anderson dies. You notice that infact you are bleeding where captain anderson got shot.
9. If you choose to destroy the reapers. You have rejected the indoctrination. You see a video of sheppard laying in rubble(Looks like the place where you got shot by harbinger) and catching breath.
Those are some of the main points of this video. If this is true bioware is pure genius. If they planned all this from the start they could add a new part after sheppard wakes up and continue the game towards the ACTUAL ending.