User blog comment:Awayorafk/Believe. The Indoctrination Theory./@comment-24690708-20160813153458

The indoctrination hypothesis does not hold water for one very simple reason: nobody Shepard met ever brought it up. There are plenty of people in the games who could have noticed but didn't say anything about it. In ascending order of suitability for detecting indoctrination IMO:

David Archer: The Lawnmower Man autistic savant in Project Overlord got Shepard into his little virtual reality world and touched her mind directly (My last playthrough was with a female Shep, so *she* henceforth). He'd have had a good chance of spotting something amiss.

Normandy miscellaneous crew: Garrus, Tali, Ash/Kaiden, Joker, and others have been with Shepard since the beginning. To a lesser extent Admiral Hackett and Captain Anderson. Nobody noticed any changes in Shep's personality. And the symptoms of indoctrination do not fit. They include intense paranoia, but even the renegadyest Shepard still places a huge amount of trust in her crew, right to the end.

Javik: Protheans can be fooled by indoctrinated sleeper agents, but even so, his weird pheromone mind reading makes him hugely perceptive.

Dr. Chakwas: You can't tell me that the Normandy's physician, once having found about about indoctrination, would not be on the lookout for symptoms or study means of dealing with it.

Liara: She does the Asari mind meld several times with Shepard to make sense of the Prothean beacons, and a few more times if you're dating her. She senses no changes in Shepard's personality.

Legion: Same reasoning as David Archer, but Legion is in an even better position to spot something wrong in Shepard's brain when they're in the Geth server on Rannoch. Unlike David he's sane, has a better familiarity with Reaper code, and has the foresight to be on the lookout for things like this.

Vigil and Victory: The Prothean VIs were able to sense Saren and Kai Leng's indoctrinations respectively, yet had nothing but nice things to say about Shepard.

The Leviathans: These big guys are masters of indoctrination themselves, being able to control people with their spheres and even reprogram Reaper husks with them, and ferociously paranoid about the Reapers- rightly so. It's a near certainty that they would notice and yell about it if a partially indoctrinated primitive came down there to chat with them.