FirstBlood XL wrote...
-Snip-
Indoc has just as many flaws.
-Indoctrination isn't something you can 'break free' of through willpower, particularly if you've just been shot by a Reapers' laser.
-Indoctrination manifests itself through feelings of being watched to eventually hearing alien voices in your mind, which the codex says is pretty much the last stage. Not only is there no foreshadowing of this (dreams are just that - dreams. They don't indicate anything other than Shepard being haunted by the death of this one child), but the games and codex have never given any indication that indoctrination leads to full-blown hallucinations.
-Indoctrination does not just happen instantly. It takes time. Given the lack of previous indications of it, it cannot just happen instantly because Harbinger is near.
-Bioware wouldn't end ME3 before the ME story is over. In all the indoc theory endings, the Reapers are yet to be defeated. Bioware isn't going to one of their most succesful series, one of the highest rated series of all time, without ending the story.
-Bioware wouldn't play the same cutscenes in both the 'success' ending and the 'failure' ending. Its just illogical.
-The 'true' ending of Shepard waking up disproves the theory. Shepard is clearly somewhere else when he wakes up - he is surrounded by large piles of rubble, whereas the land in front of the Conduit is pretty flat and scorched. Not to mentioned bathed in a blue glow. This means either the rubble has appeared from nowhere, in which case the Conduit has been turned off (Shepard fails in eveyr ending if this is the case, which Bioware wouldn't do) or Shepard is still indoctrinated (again, every ending leads to Shepard failing). If Shepard had been moved by any of his team, they wouldn't have just abandoned him on a pile of rubble, and if he had been captured by the enemy, again they wouldn't have just left him lying around on his own.
-The game outright tells you that, in what you just played and saw, that Shepard ended the Reaper threat. Not that he will go on to do so later, or that the next Cycle uses Liara's beacons, or that someone else enters the Citadel and ends the Reeaper threat, or that you will end the threat in DLC, but that in what you literally just played and saw, Shepard ended the Reaper threat. This is simply not the case if the indoc theory is true.
Does the theory have less plotholes than the real endings? Yes.
Does that make them right? No.
Both the real endings and this theory are full of holes in both logic and lore.