User blog comment:The Milkman/The Writing of the Ending/@comment-30764484-20120605044952/@comment-30764484-20120605161555

Two important points about IT that a lot seem to be confused about.

Shepard is not indoctrinated UNLESS you choose control or synthesis, because choosing control is symbolic of thinking like the Illusive Man, and choosing synthesis is symbolic of agreeing with Saren and the Reapers. If Shepard chooses to say no to the Reaper's logic, and symbolically choose destroy, then Shepard was never actually indoctrinated at all.

Object Rho simply accelerated the indoctrination process, it didn't indoctrinate Shepard. And like it or not, Arrival is canon, because one of the comics talked about Shepard destroying the relay. You can choose to play without Arrival, but that's a non-canon alternate reality. Just like it's canon that Anderson is made councilor in ME1, because it's in one of the novels. You can also choose Udina, but once again, it's non-canon.