It seems to me that indoctrination falls into one of the following flavors:Mr. Gogeta34 wrote...
It could be two different methods to the same goal: controlling organic minds.
Some control can be over motor and speech functions, while another (likely higher) type of control is exerted over the person's will as well.
But that leaves a large plot hole if we infer that such control means indoctrination. Because Shepard was clearly under TIM's control through Reaper technology... so why didn't the Reapers defeat Shepard? Why control just TIM when Shepard is more valuable at that crucial point?
If the answer is that Shepard's not indoctrinated... back to the original question: "Why wasn't Shepard Indoctrinated?"
Direct Control (total possession) - 100% of brain functions are Reaper controlled. The victim has no willpower, and in fact, I suspect the victim's identity is completely unconscious at this point; it's all Reaper in there. If the Reapers release their grasp, the victim probably wouldn't remember any events from when he/she was "under" - like the Leviathan thralls.
Temp Control (simple motor control) - this is the "It's like beating your hands on the glass while watching yourself" experience. The victim's still conscious, and if it's a rapid indoctrination, he/she might struggle for control. Long-term victims, like Dr. Kenson, might not fight it, because they've been brainwashed to accept the Reapers' POV. (She wants to see the "blessings of the Reapers.")
Psychological manipulation (brainwashing) - torment the victim with visions and whispers to mentally exhaust them and wear down their will. Thought insertion, where the victim "hears" an idea in their head and believes it to be their own. Emotional manipulation. The victim becomes a "willing slave," but if he/she "sees" the manipulation and starts to fight, the Reapers may assume control, if their connection's strong enough. These are the long-term, sleeper agents.





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