User blog comment:Suparockr/List of Plotholes throughout the series/@comment-166.82.245.89-20120719070005/@comment-1440333-20130301001240

tl:dr

basically the indoctrination theory, like ANY twist ending, be it in games, cinema or literature, invalidates and undermines the entire plot, creating more plotholes than it solves. Twist endings never work - Look at Sixth Sense: Bruce Willis has been dead the whole time. are you seriously telling me that over the course of several months he didnt notice this? No-one talked to him, so he couldn't get served in a shop or restaurant - where does he eat? His widow certainly isn't making meals for him.

In ME3 the IT says Shepard has been indoctrinated. This is never hinted at across all three games. Shepard is never near Reaper tech long enough to be indoctrinated without causing him to become a gibbering wreck, which the codex basically says that rapid and forced indoctrination does. The whole idea cannot possibly work.

Shepard either dies, ascends, breathes or merges with all life - four options that follow brilliantly from the themes and plots already in the series and expanding on them. The IT spits in the face of all those themes.