Everything after you get hit by Harbinger's laser takes place inside Shepard's head.
TIM's choice (Control) and Saren's choice (Synthesis) are presented by the kid as the good choices, while he presents the 'destroy' choice as the bad one. That's of course only an interpretation, but if you listen to his dialogue I think you'll agree.
The kid is a Reaper (harbinger?). He says "I know you've thought about destroying US"
If you listen very carefully to the kid's dialogue, you can hear that Jennifer Hale and Mark Meer are also reading the lines. I'm not making that up. Jennifer Hale is in the left ear, Mark Meer in the right. That further suggests that it's just inside Shepard's head.
When you pick Synthesis or Control, Shepard drops her gun, which is symbolic of giving up. In the Destroy ending, Shepard shoots the power conduit, which makes no sense in the context of triggering the crucible, but it's a rebellious act and represents Shepard breaking free of Harbinger's attempt to indoctrinate her. If you pick the Destroy ending and have high enough EMS, there is a cutscene where Shepard wakes up in London.
Indoctrination is described in the codex as making the indoctrinated think that the Reapers are divine, that they have a good purpose and that you must help them. Throughout the games we also learn that it causes strange dreams, and hallucinations, ghostly images etc.
Shepard's dreams could be PTSD, but it could also be the Reapers beginning to invade her mind. Each dream gets increasingly dark, and in the later ones you see those black smoke pillars kinda shaped like humans. When TIM is controlling you in the end, you see kind of similar black lines invading the screen. It's not super similar, but maybe something.
Also, throughout ME3 there is a constant theme of questioning Shepard, whether she's herself, if she's felling alright, if she's still Cerberus etc.
Some people also speculate that the kid is a pure hallucination from the beginning. He runs through a locked door into the house that gets blown up, after he says "you can't help me" (which is a weird line for a kid), Anderson calls your name and you snap out of your thoughts. Strange reaper noises can be heard at that point (quite different from the other ambient reaper noises). In the 3rd book that's described as happening when Greyson is fighting his indoctrination. Furthermore, no one seems to ever interact with the kid, or even notice that he's there. When he boards the shuttle, no one helps him even though it's a freaking kid! Everyone else gets helped aboard.
Wow that actually makes more sense than anything I've come up with.
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