User blog comment:Raymorn/Bioware Co-Founder Dr. Ray Muzyka Speaks Out/@comment-3148237-20120322021617

Major problems with the Indoctrination Theory: 1) Indoctrination always seems to occur gradually over a period of time (e.g., see Dr. Kenson's. log entries). There's been no indication that Shepard's exposure to reapers/reaper tech so far has been enough to indoctrinate him, even somewhat.  That means Shepard would need to have been indoctrinated extremely quickly (i.e., right at the end of the game) for the theory to hold up. 2) If it is possible to indoctrinate someone that fast, then why don't the reapers just indoctrinate everyone they come in contact with rather than battle it out with organics?