Dwailing wrote...
OK, I'm going to add my little bit of speculation regarding the Conduit/Decision Chamber overlay from yesterday. This fits with Waking Nightmare Theory. (Heads up, wall of text incoming.) My wonder now is, given how well the two match up, maybe Shepard had STARTED breaking free from the indoctrination attempt after the Anderson/TIM scene, and was actually awake but in what is a more literal hallucination (I.E. He's seeing things that aren't there or he's seeing things that are there but he's just not seeing them as they really are.). Now, if so, then this would open some new possibilities.
That would make the Synthesis beam the "Conduit" beam. Which means that Shepard would be thrown into the Citadel (The force of the impact from being sent up there being enough to wake him up.), indoctinated (Because he chose Synthesis.), and he would open the arms and dock the Crucible (My personal beliefs are that the Crucible is some kind of Reaper trap and they needed all the fleets in one place to use it to its fullest potential. That would explain why that brought the Citadel to Earth.), securing Reaper victory.
In Control, Shepard might be walking over to some kind of electrical panel on the side of the Conduit, and if he grabs it, he'll be fried (And indoctrinated for choosing Control.). At this point, he'd snap out of the hallucination, and he'd be indoctrinated (And possibly in very bad condition.). Then, even though he'd be too badly wounded to go to the Citadel (Due to being fried by large amounts of electricity.), he could be evac'ed to receive medical attention, and he could be used as a sleeper agent.
In Destroy, Shepard would walk over to some kind of conduit or explosive of some sort, and he would shoot it, presumably, with a Predator. The pain from the explosion combined with his resistance of the indoc attempt would snap him out of it, but he would be buried under rubble and pretty badly wounded, and he would have to be found by someone else. This could be why the kid presents the choice of Destroy. Even if Shepard's will is too powerful to succumb to indoctrination (This is Destroy after all, it's definitely a way to break free from indoctrination.), he can still hurt Shepard when he breaks free.
Finally, Rejection. In Rejection, Shepard realizes, at least subconsciously, that something is wrong. So, he refuses to take any of the choices. This has two consequences. On a mental level, Shepard has broken free from indoctrination by refusing to take any of the choices presented by Star-Brat. However, Shepard has NOT received any kind of jolt to snap him completely out of the hallucination. So, now, Shepard needs something to snap him out of it. This could be his LI, Anderson (In the event that he doesn't have a LI.), or someone or something completely different.
Now, I know this is a wild hypothesis, and I acknowledge that it might not be the most likely, but I think that something like this would work pretty well. Also, I give due credit to Arian Dynas for the idea about the "Control" panel 
being some kind of electric thing (It was in his ending script.).
Bumping for speculation.
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I don't know why people keep saying it is. 
Anyway, I'm going to repost a hypothesis that I had a few pages ago that could explain the similarities between the run to the beam and the decision chamber. It also presents a hypothesis for what Rejection is.
