User blog comment:SilencedSkies/The Illusive Man: Good, Evil or just bad writing?/@comment-1484665-20120412024804/@comment-3325589-20120412061550

We don't know he wasn't indoctrinated before the more obvious implantation. He'd been working with and around Reaper tech for months before that (Paul Grayson, the Reaper implants on Cerberus soldiers, the Reaper communication experiments, etc.), and it's entirely possible that he was in contact with it enough to become indoctrinated. Kai Leng is an example of a major character we know is indoctrinated, but who doesn't look as obviously Reaper-y as Saren or TIM on the Citadel. I mean, he has those weird goggles, but those aren't more of an obvious red right hand than half of Shepard's headgear.