There's also the events of the Invasion comic to consider - I haven't had a chance to read it all yet, but based on the overviews...Setrus said:I believe Bioware has stated that the Illusive man is NOT indoctrinated. That said I believe his minions just might be. (his own mind-controlled slave army, oh how quaint...) So why would he fight you then? Well maybe because he doesn't see fighting the Reapers as a viable choice, that humanity must take a new form as a Reaper and Shepard is in the way of that? Or maybe the same reason as Saren before he completely lost it, that only by working with them can he make himself useful enough to spare. I remember that doctor Breen in Half-life helped the combine by making humans seem useful instead of letting humanity be destroyed... *shrugs*
...Cerberus took over control of Omega from Aria at some point between ME2 and ME3, and has been using it as a base of operations to diddle around with Reaper technology beyond the Omega 4 relay. And we all know how well diddling around with Reaper technology normally works out.
Plus whether or not he's indoctrinated, he's definitely been in contact with a Reaper artifact similar to the one Shepard encountered in Arrival.
Anywho, I'm still confident it'll all be explained in-game.