M U P P 3 T Z wrote...
i'm not a fan of this theory, since it suggests that Shepard has been indoctrinated either before the start of ME3 or throughout the entire game -- but HOW? You can say that there is a secret indoctrination device on the Normandy, his implants, etc. etc. But I personally don't find that compelling.
The indoctrination could have started as early as Vrimire. Sovereign was present at the base, since Saren was using it to research the effects of indoctrination on the Salarians he had captured. You also talk to Sovereign via the platform on the beacon and I think no matter where the Reaper is, you can still be indoctrinated just by hear its voice.
At the end, Shepard is once again in proximity of Sovereign while fighting Saren, being further exposed to the effects of the indoctrination signal. Then Shepard spends two years dead and being rebuilt, with the inclusion of cybernetics for parts that couldn't be regrown or repaired. The next time Shepard is anywhere near a Reaper is the derelict Reaper you go to and the logs of the Cerebrus team that had been there proves that even the derelict Reaper was still emitting an indoctrination signal, further exposing Shepard.
Shepard was exposed, but not consistently enough where he was indoctrinated in the fashion that Saren, Benezia, and TIM are. The effects were still there, but Shepard's will to continue to resist them kept them at bay up until the end, when Harbinger go tthe opening it needed.
Pure speculation but take it as you will.