GBGriffin wrote...
The more and more I hear about this theory, my hopes get raised higher and higher. If it's true, it'll blow my damn mind.
Again, are there any arguments that would refute this idea? Preferably without breaking down into a flame war? 
Yes, SO many.
1) Indoctrination
does not work that way. It
cannot put you into a gigantic, highly elaborate hallucination world. Indoctrination that convinces people that they're doing the right thing and defeating the Reaper threat when they're actually helping the Reapers takes time--quite a bit of time, and potentially even implants if the subject is resistant. Even then, it's not guaranteed (ask Saren).
2) Indoctrination also has distinct symptoms--irregular headaches, a "ringing" sound being heard all the time, "voices" in one's head (usually in the form of whispers), decrease in mental stability, and more. Shepard exhibits none of this at any point.
3) There is no "metaphorical" battle against indoctrination. It's like resisting psychological torture--you don't "win" in some highly detailed, massive metaphorical hallucination, you "win"
in reality.
4) If the Reapers were in a position to induce some crazy (and crazy fast) indoctrination onto Shepard,
they were capable of killing him outright. And there's no gain to a risky attempt at indoctrination. It's also most definitely not a "passive" attempt at indoctrination, as it's on a whole different level than any other kind of indoctrination.
5) Super-fast/super-intense indoctrination--which still takes time--results in very fast mental degredation, reducing its victims to mindless/braindead meatbags within a matter of hours (a few days tops). Shepard sure as hell isn't undergoing any kind of mental degredation, seeing as he's capable of talking TIM into suicide. He's also capable of fighting a Marauder and husks in his seriously wounded and dazed state.
6) The "Destroy" option is available in the first place. In fact, it's the only option that's
guaranteed to be available to the player, no matter how low their EMS, which makes no sense with regards to this "hallucination" theory.
7) If the player chooses "Destroy", he/she only sees the "survives" cutscene if he/she has a very high EMS. Whether or not Earth gets destroyed also depends on EMS. So...?
8) Shepard "wakes up" in the "survives" cutscene in broad daylight. In other words, HOURS later. So by then, the Reapers have already either won or lost. So...?
9) And more, but it's kind of moot at this point. Fact is, I really
want this "hallucination" theory to be the case
across the board so that some new ending can be tacked on. That's really what is needed, here.
It's also just plain bad writing and effort. If it was all actually a hallucination, they should have included the other stuff
in the game.