Irridium said:
Where the hell is everyone getting this "TIM is indoctrinated" stuff? I've found no mention anywhere of it. Sure Cerberus team members get indoctrinated, but not him.
It's from the Mass Effect: Evolution comic. TIM finds reaper tech and some turian husks while on Shanxi. One of his men tries to deactivate the reaper device, and gets zapped, turning him into some kinda husk. TIM tries to save him, gets zapped a little himself, and winds up with some neato cybernetics (hence the eyes).
I haven't read the comic myself, but I remember hearing about it from somewhere. I don't think he's indoctrinated, but it wouldn't be too far off to think he is influenced in some way by the reaper tech.
edit: http://masseffect.wikia.com/wiki/Illusive_Man#Mass_Effect:_Evolution