FalconRising wrote...
Playing devil's advocate in the interest of promoting discussion. Apologies if this was covered somewhere in the preceding 659 pages.
-TIM appearing on the Citadel
I'll point out that before this point, you haven't seen TIM in person for a very long time, if you actually see him in person anywhere in the game (I fear I can't remember). He even left his own space station before you showed up. We know for a fact that he's indoctrinated from the Prothean VI's dialogue, and we've seen recorded footage of him receiving Reaper implants. It's not much of a stretch (given what we're already accepting) to imagine that he can manipulate the image of himself before it's sent out via quantum communications, and that he moved to the Citadel around the same time or maybe even before he warned the Reapers of Shepard's thrust against Earth.
-The secret cutscene of Shepard breathing
There's nothing wrong with this, but I'd like to point out that the Destruction path is the only choice where Shepard's body isn't disintegrated on camera, which makes it the only path that could logically contain said cutscene, whether you subscribe to Indoctrination Theory or not. In other words, if the events on the Citadel are indeed actually happening, that cutscene can only follow that choice, so I don't think Destruction can be inferred to be the right or happy ending on the basis of the existence of said cutscene. It can be argued that disintegration is symbolic of successful indoctrination, but I feel that source material that easily goes either way like this doesn't make for strong support.
There are screenshots/video of Shepard's eyes strongly resembling TIM's for an instant during the Control path. To me, if this means anything, it means that TIM was indoctrinated long before ME2, which is a whole new can of worms.
-The so-called "Ilos Run"
The radio chatter here is not significant either way. They clearly think everyone making the charge died, including you, and no one is alive or otherwise able to report that this assumption is inaccurate. I admit I have no idea why this Carnifex suddenly has infinite ammo, but I think this can reasonably be explained as BW trying to make this part feel super epic (like the end of COD4) but doing it in such a way that made people question the story instead. Adjusting HP such that each Husk dies in 1 shot and the Marauder die in 3 shots, and having you die if you miss, would have been a less obtrusive way to do it.
-Choosing Indoctrination
I hope I don't mind**** anyone, including myself. Here goes. I find it kind of hard to believe that if the events on the Citadel are Shepard's mind's interpretation of Indoctrination, then the path that equates to resisting indoctrination is the path you've been working towards all along. I'll elaborate; if indoctrination is the type of control you have to choose to accept, on whatever level, it makes more sense to disguise that acceptance as something the subject is known to be receptive to. Reaper files on Shepard must be extensive, they know s/he's working to destroy them. In other words, if all of that is a hallucination intended to indoctrinate Shepard, then to me Destruction seems the most likely to lead to indoctrination, as Shepard's mind has accepted the fantasy - after all, it came to Shepard disguised as the goal Shepard's been working towards all along. In fact, if this the case, then it's likely that choosing any of Destruction, Control or Synthesis within the confines of the hallucination leads to Shepard's indoctrination, and the only way out would be to shoot the god-child/AI, shoot yourself, or something else that reflects exertion of your will over that of Sovereign's. This is all, of course, assuming our understanding of indoctrination is accurate.
-Things I don't have answers for
How Anderson got to the panel before you.
How the Normandy is making a mass relay jump when it should be supporting Shepard on Earth.
How your squad suddenly got aboard the Normandy.
Why there are human letters/numbers in a part of the citadel no organic has ever been to before.
Why we, the players, are seeing cutscenes of things that might only apply to a hallucinated game world.
tl;dr
The source material contains reasonable explanations for TIM being on the Citadel, Shepard's breathing cutscene, and some parts of the "Ilos run". There are other loose threads, but without these three points I don't feel Indoctrination Theory holds water. I'm sure I didn't comprehensively answer all of the points raised by Indoctrination Theory. I hope this leads to a stronger discussion.
Thanks for reading.
I have to strongly disagree with your assessment of the Shepard breathing scene. I get that the 'Destroy' ending is the only one in which we don't see Shepard disintegrate, but how could Shepard survive the Citadel's destruction?