Hm potential reasoning for Indoctrination throughout the game.
Seeing as Shepard has been near and in direct contact with Reaper technology it's not impossible that the mark of indoctrination is somewhere in your mind but not in an ample enough a manner for you to become a husk, or maybe you are too resistant to it's affects.
Once the Reapers land on Earth they attempt to take control of Shepard through this "mark", this is when you see the boy in the vent who seemingly disappears. Shepard's mind is somehow too much for the Reapers to take direct control of, you resist where NO OTHER organic in existence has and continue on your mission to rally the galaxy.
The Reapers may be surprised, but not unprepared. They continue to attempt taking direct control of you when you are feeling weak or stressed, sending their indoctrination signal in forms of your Nightmares. Nightmares that get progressively worse, potentially the Reaper signal getting stronger. The only thing that wakes you is the shock of seeing the boy engulfed in fire, and yourself engulfed in the last nightmare as well. Possible the fire is your mind/willpowers way of warning you, snapping you out of indoctrination.
The Illusive Man is obviously indoctrinated, everything he says and does is what the Reapers want him to do. They allow him discover their control signal, allow him to figure out how to implant a means to emit this control signal in some kind of cybernetic implant (you can see him getting ready for some kind of surgical procedure in a video log in his base).
Harbinger sets the stage during the Beam run, grazing Shepard enough to nearly kill him/her when it can just as easily make Shepard into dust with it's cannons.Shepard is weakened enough for The Illusive Man (perhaps from the Citadel while Shepard is unconscious) to act as a signal booster to assume control of Shepard.
Shepard "wakes up," but is really still fighting off indoctrination from that point when you open your eyes and grab that Carifex hand cannon, everything preceding is your struggle against the Reaper signal. The Illusive Man, implanting himself in your hallucination, does is best to convert you to his way of thinking, he "needs you to believe," him, therefore, the Reapers need you to believe them. Anderson is there as a manifestation of your willpower, when you are forced to shoot him, you begin to bleed out from the same wound. You can convince The Illusive Man through paragon dialogue that he is indoctrinated, he will opt for shooting himself and potentially killing himself in the real world, "the body cannot live without the mind." Through renegade dialogue or action you can shoot him yourself. Both of these result in his death and puts a stop to the "signal boost" he provided, allowing you to progress in the hallucination as desired opening the Citadel arms and relaxing next to Anderson. Anderson, or your willpower, was gravely wounded by TIM's indoctrination, he therefore served his purpose in weakening your will. TIM's death WOULD NOT end indoctrination since the Reapers are the true power behind the indoctrination signal.
Anderson/your willpower dies, and you pass out crawling to the Citadel control panel. This is what the Reapers wanted, and they assume full control over the indoctrination attempt thanks to TIM. The Catalyst gives you three choices, each of them with odd explanations. Everything about the room seems surreal, your own voice coming from the Catalyst, the echo in the room, the Catalyst appearing as the child you failed.
You pick the blue option, you appear to become a husk with The Illusive Man's eyes (something I relate to being a Reaper agent now.) And the last of your will dies as you disintegrate in dream. When you awake in the real world, your body and it's unique ability to resist the Reapers now belong to them.
The green option is much the same, though I view it more as leaping directly into the Reaper's influence than trying to take control over it. It ends with the same result as blue.
You take the red option. The only choice that seems sane, you go out gun blazing defeating the Reapers in your hallucination despite the potential consequence to the Geth, EDI, and yourself, "Even you are partly synthetic." You will overpowers the Reaper's influence. You wake up in the pile of rubble on Earth, near the Beam, nearly dead from Harbingers attack. But you still draw breath.
Resiting the elaborate indoctrination attempt may even cause the entire Reaper fleet to stumble for moments, precious moments that the Allied fleet can use to decimate Reaper numbers. Similar to when you defeated the possessed Saren in ME1, Sovereign assumed direct control of his corpse and with his defeat Sovereign was stunned just long enough to be destroyed.
I hope to see something alluding to this in Extended Cut, but we can only hope.
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