User blog comment:Arbington/ME3 Theories/@comment-217683-20100809035138

I dunno about Reaper indoctrination of the Illusive Man. His actions and behaviors in the latest novel seem to pretty definitively rule that one out. As for being peeved about the Collector base getting blown up, that's simple to explain without Reaper indoctrination. Keeping it in Cerberus hands would have greatly strengthened his organization, and by extension, humanity (if you buy into Cerberus' ideals). So yeah, I'd be willing to bey quite heavily that the Illusive Man is not indoctrinated. At least, not during and just after ME2.