User blog comment:The Milkman/The Writing of the Ending/@comment-30764484-20120605044952/@comment-30764484-20120605163744

Indoctrination worded another way is simply an individual agreeing with what the Reapers want. If they can't convince said individual, that individual is not indoctrinated. So far no one has had the willpower to resist the Reapers' ideas, they get to you, in some small way. They appeal to what you want. The Illusive Man wants to help humanity, whatever the cost; that was their door into his mind, convince him doing certain things that really help the Reapers are in his intrest. No one knows they're indoctrinated, or being indoctrinated, that's the point. If we as players had know what was really going on, it would have ruined the whole thing. They weren't just indoctrinating Shepard, they were indoctrinating YOU. If YOU pick synthesis you're agreeing with the Reapers. If you agree with the Reapers, you're indoctrinated.

No, indocrination is not all of a sudden, but there will be a tipping point, a point where something will finally click in your mind and you'll "see" the Reapers' "logic". It's just like figuring out anything else, like when you can't understand something, then all of a sudden you just get it. It's like that.