So, I recently finished Mass Effect 3, and then just today decided to Google the ending to see what others thought about it. Of course one of the first things I came across was the "indoctrination theory." While I have actively avoided spoilers about Mass Effect 3's plot until I got around to finishing it, I'm sure that many are aware of this theory by now. What kind of blows my mind is the number of people who actually deny it. I suggest they watch this video, if they haven't.
Now, of course I had not thought about all of these points, but once Shepard set foot inside a Reaper ship, I began to suspect that the Reapers were going to try to take control of Shepard. I think I had considered it even in the first game, but actually going into a Reaper ship was the thing that really made me strongly suspect it. Even early on in Mass Effect 2, though, I toyed with the idea that the new Normandy was actually a Reaper ship, and l that the Illusive Man was actually a Reaper creation. As for the third game, why is the Illusive Man always a step ahead of Shepard? Is he really just that amazing? (I'm kind of reserving judgment on all that until I play through the trilogy again, but regardless of where the ship actually came from, the Normandy does at least have a Reaper part by Mass Effect 3 (and with that being a plot device, that also means that the ship probably did not actually have anything to do with the Reapers before that point.)) Anyway, after watching the video linked above, I'm firmly convinced that not all is as it seems. Just how much, I'm not entirely sure. I am quite sure of two things, though:
1. The child that Shepard keeps feeling guilty about throughout Mass Effect 3 is not real. There are too many clues for that not to be the case, but it's really the ending that rather seals the deal here.
2. The stuff that happens after Shepard gets back up and heads toward the beam to get to the Citadel is not real. It is an internal battle against indoctrination. There are many indicators here, as explained in the video, but perhaps the biggest giveaway is that it makes no sense at all for Anderson and the Illusive Man to be on the Citadel. Actually, there is a bigger tell, but many might not witness it, and that is that if you choose the destruction ending (the "correct" path to fight indoctrination) with a high enough galactic readiness, there is a brief cut of Shepard still alive under some rubble.
I would also like to bring up another point which I do not think was brought up in the video, something that I was thinking about long before the trilogy ending: The Citadel is, as far as we know, a Reaper invention. Doesn't it logically follow that the Reapers would use the Citadel itself to indoctrinate those who are on it? I'm not too sure about that, but consider the overall behavior of the Citadel Council with regards to Saren and the Reapers from the very beginning, and the behavior of Earth's recently appointed Council member, also. That is something that I was thinking about for a long time. Are we just supposed to pass it off as a mere coincidence that the galactic center of power is in one of the Reapers' largest (that we know of) creations? A creation that is already known to be even more significant to the Reapers than anyone initially suspected? I don't think so. (Actually, I think it was pointed out in one of the first two games how that is part of the Reapers' plans, but I don't think anything was said about it being used for indoctrination.)
So basically, Mass Effect 3's ending, while, upon further inspection, not offering much closure, is quite a bit more than people initially gave it credit for. (Yes, I know they added to it with DLC, also.)