User blog comment:Awayorafk/Believe. The Indoctrination Theory./@comment-1341687-20120909223238/@comment-1341687-20120910035838

Indoctrination wouldn't happen in a flash like that. If it could, then there wouldn't be a resistance on any planet. To claim that it happens quickly in Shepard because they are focusing on him is silly. At that point it's just looking for a macguffin in an already convoluted and non-cohesive theory. Because they could have done it at literally ANY point and saved themselves the trouble.

If indoctrination occurs over a long period of time (as we have been shown in each game) or isn't obvious ala Rana Thanoptis, then it could be detected regardless of stage. The Reapers have influence over you, no matter how small. They wouldn't have waited to the last second to TRY and indoctrinate him.