The Invisible Commando wrote...
I don't see how people are still talking IT theory that I never believed. The StarBrat comments himself that TIM could never use the control method himself because he is indoctrinated. Obviously if Shepard is indoctrinated he can never control the Reapers. Also if he was indoctrinated, he would be a puppet. Why even give him the illusion of choice? StarBrat could just order him to do whatever. The IT theory logic is flawed even by the game itself.
i think IT states that talking to the Star Child at the end is the final step to becoming completely indoctrinated. I *think* from what I understand - Shepard is still on Earth during the end of ME3 (when you confront Illusive Man and Star Child), and the events are all taking place inside Shepards mind. He is fighting the indoctrination process (hence why he can stop Illusive man). Anderson (which represents Shepards ideal of right and good) congratulations him/her for doing the right thing, and the Reapers force Shepard to pass out. Star Child intervenes and tries to convince Shepard that Destroy is the worst option, while Control and Synthesis are best. Shepard sees Anderson "destroying" and if he chooses the other two he dies. However, if he does the *right* thing and destroys, he wakes up back on Earth, and has overcome indoctrination.
Future DLC will expand on the ending and give us a REAL conclusion I.E. shep wakes up and beams up to the Citadel, finds himself in the council chambers, activates the Crucible and sends out a signal shutting them all down. He returns to Earth, and the galaxy is saved. Whether Anderson and co. survived the assault from harbinger is unknown.