The theory is that, all through the game, the Reapers are indoctrinating Shepard in the same way that they attempted to indoctrinate Saren -- by making Shepard think that a compromise must be made in order to ensure the survival of the galaxy's civilizations. And by slowly cutting away at Shepard's sense of hope against adversity. Everything after the run to the beam in the final level is an indoctrination-induced hallucination. Arguments and observations:
* Shepard's prolonged exposure to the Reapers throughout the game means that she's constantly within range of their indoctrination signals.
* And even when she's not around them, the Reapers technically uploaded a virus to the Normandy in ME2. EDI locked it down for the rest of the game, but there's also no proof that it was completely eradicated, and its full effects are not explained, meaning that the Normandy itself could be serving as a tool of indoctrination even when Shepard is away from the Reapers.
* Vega mentions there being a "hum" on the Normandy -- which was a trait of indoctrination tech.
* The child is meant to be a representation of all Shepard's guilt over not being able to save everyone, eating away at her confidence, sanity, and sense of hope. The child is merely a hallucination, right from the very beginning. Thus the unnatural, ominous, "you can't save me," line and the abrupt disappearance from the vent shaft, complete with no noise associated with the child running away in a vent.
* The dreams, therefore, are manifestations of the indoctrination. The final dream, showing Shepard being consumed with the child, has two possible meanings. The first meaning is that it's Shepard's final descent into lack of hope -- and she assumes that she'll join her dead crewmates in the afterlife even if she's victorious. The second meaning is that it's Shepard's subconscious rebelling against indoctrination, offering a warning that going with the child will result in doom.
* During the run to the Citadel beam, your squadmates do not run with you. They stay in place behind you, unmoving, regardless of what orders you give them.
This is where the game's real events stop. Shepard lies in the rubble unconscious in front of the beam and descends into an indoctrinated hallucination.
* If you have a low war asset score, your team is seen dead near the beam, far ahead of where you were. Shouldn't be there if they stayed back. The image of your dead team is a deliberately heavy-handed demoralizing scene -- pointing out the futility of trying to resist.
* Shepard has a totally different sidearm after being struck by Harbinger, and it has infinite ammunition. You also switch over to having ruined N7 armor, regardless of which armor you were actually wearing.
* Shepard goes through the beam, but Anderson - despite not even being in the immediate area - also goes through. BEFORE Shepard.
* Only human remains are piled up along the Citadel corridor and in an unnatural fashion. Anderson (Shepard's subconscious at this point) likens it to the Collector base.
* Anderson describes the Citadel walls as "moving, realigning, reshaping themselves." This is the same sentiment expressed by the indoctrinated workers who were on board the Derelict Reaper in ME2.
* The Illusive Man is inexplicably there already too. Anderson and the Illusive Man are manifestations of Shepard's mental war -- the devil and angel on her shoulders.
* The ensuing argument involves a lot of black lines warping over the screen -- and a robotic growl every time Shepard starts to gain clarity. Another symptom of indoctrination according to game lore. Reapers growl when they feel their subjects aren't listening to them.
* It's never made clear who is controlling Anderson and Shepard at the end - TIM or the Reapers. The Illusive Man is not subject to it, but he also makes no gestures of being the one pulling the puppet strings. The Illusive Man is what the Reapers want. They want someone to be stupid enough to try and control them, only to dominate/incinerate him at the end. Anderson only wants to blow them up, and so he must die/suffer for his resistance. And so will Shepard, if she doesn't know what's good for her.
* Upon ascending to the final chamber, Shepard is in EXPOSED SPACE with no helmet.
* The Catalyst takes the form of the child to continue manipulating Shepard. It insists that synthetics will always rebel, but the geth and quarians are now proof that they can get along. The Catalyst is an unreliable narrator trying to convince Shepard that the Control/Synthesis choices are the only way to resolve the conflict peacefully, and that Destroy will involve wiping out EDI and the geth. There's no proof of that, though, and why should you obey an AI associated with the Reapers? Unless you're indoctrinated and believe whatever it's telling you.
* Control not only kills Shepard, but there's no guarantee Shepard can actually control them once "assimilated." Synthesis makes everyone partly synthetic, which still leaves the Reapers at the top of the food chain, and it's easier for the Reapers to take control of synthetics (geth) than organics. In these two endings, the Reapers theoretically win because
Shepard tried to compromise with the devil in the same way Saren did.* The Destroy ending is the only ending the AI seems to warn against, and it's the only one where he really lays on the guilt. Meaning that's the one the Reaper AI doesn't want you to pick. Saying that again - it's the one that the Reaper. AI. doesn't. want. you. to. pick.
* The Destroy option is also painted in "renegade red," but shows that it's Anderson's choice. The Control option is "paragon blue," but it's the one that the Illusive Man wants. We've completely swapped roles at the drop of a hat -- deliberately misleading.
* The "full" ending exists only with the Destroy option. It shows Shepard -- still in armor -- waking up in rubble. Earth's rubble. Not the Citadel's. Indicating that Shepard either got beamed back down without explanation, or that Shepard had gotten knocked out by Harbinger's deathray and was just now waking back up after the hallucination.
* Shepard, then, effectively wakes up from indoctrination, whereas the other two endings promote Shepard giving up. It implies that Shepard will finish the mission, even if we don't get to see the "real" ending.
* The final "battle," then, is the player deciding whether to give into indoctrination and follow the AI blindly, or recognizing that stuff is royally messed up and something is wrong. And part of the battle is recognizing the signs of indoctrination that have been described throughout the series.