While the indoctrination theory has merits, one thing clearly stands out for me. At the end of the game when Shepard is discussing the control aspect, he says "So The Illusive Man was right after all." To which the child thing says "Yes, but he could never have taken control because we already controlled him." To me, this implies that TIM was indoctrinated and Shepard was not.
Biggs613
this is super late lol, but Shepard WAS indoctrinated, not fully, but he was. The harbinger purposely implied to Shepard that the illusive man was indoctrinated and that he (Shepard) was not. By merely implying that and not directly stating to Shepard that he himself is not indoctrinated, it gave Shepard a FALSE sense of self thought and control, but by believing that implication Shepard proved that he didn't have as much control as he thought.
The only ending that keeps shepard alive is the RED RENEGADE option. The BLUE PARAGON option shows Shepard getting devoured in a non-peaceful way because he has became fully indoctrinated. The proof to that is in the exact words from your post... "Yes, but he could never have taken control because we already controlled him." That was true for the illusive man and it was true for Shepard as well.
This is and will forever be the greatest ending ever in media. Why? Because I played over 100 hours in my 3 save files trying to defeat the reapers and save the galaxy and what did I do in the end? I FAILED, I BECAME INDOCTRINATED and didn't even know it... and that's precisely it, you wouldn't know you were indoctrinated if you were indoctrinated lol. I played paragon for over 100 hours and the BLUE PARAGON option at the end lit up like a beacon, I thought "it's over, i won, i did it!". But what I really did was get defeated by the Reapers. That is a beautiful ending, just wow :)
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