So yeah, I along with a lot of fans believe the ending is played out in Shep's mind. That is why you awake on a load of rubble seemingly after being blown to [censored] by Harbinger if you choose Destroy, thus breaking the indoctrination. Brilliant, if it's true. I still have problems with it because there is a complete lack of closure and it cuts off the real [censored] end, presumably for DLC which is hilariously greedy.
It's still poorly written as it wrestles away almost all player control. I can pick from three potential endings, but I have no ability to further interrogate this strange, new character? If I could challenge his claims based on things I'd done/learned throughout all three games, either fully exposing the plot or at least gathering clues, it might have worked. As it is, you're simply spoon fed information and forced to accept it.
Oh yeah, and you're wearing armour as you sketch for the Conduit yet when you "wake up" you're wearing your casual attire. I'm not terribly articulate, look it up.
You are? I was still wearing my melted armor.
We can't know the Reapers' reasoning. Rather than having me try to convince you why they would indoctrinate Shepard, why don't you try to convince me about all the plotholes at the Citadel? Or why destroying the Reapers is the only option wherein Shepard survives, seemingly on the rubble of London? This one issue with Harbinger having no reason to control Shep surely doesn't disprove the entire theory to you?
The fact that you see the ending cutscene with the relays destroyed, and Joker trying to outrun the blast and crashing on some unknown planet would seem to throw that out the window. If it was indoctrination, choosing to reject the Reapers should end the spell right then and there. Why would choosing destroy result in visions that the Reapers dying and then totally nonsensical Normandy scenes? Wouldn't you simply wake up or lose consciousness?
EDIT: Looks like you ninja'd me a bit on that last point. The Reaper death scene, I could see as being a hallucination brought on by the perception of victory. The Joker/Normandy scene is way too out there to be ascribed to anything, though.