However, he was also clear about the fact that Shepard being indoctrinated was never on the cards at BioWare - it's a theory that was completely born from fans. “The Indoctrination Theory is a really interesting theory, but it's entirely created by the fans,” Hepler explains.

Is the indoctrination theory canon?

A former BioWare writer confirmed in an interview that the "Indoctrination Theory" for Mass Effect 3 isn't canon -- but not because it isn't smart.

How was the Illusive Man indoctrinated?

Depending on the player's prior in-game choices, Shepard may convince him that he is indoctrinated, which causes the Illusive Man to shoot himself, with his final words revealing that he attempted to resist the Reaper indoctrination.