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Okay, but if they kill Shepard the war is over. It's not going to continue. The Crucible will never dock, the Victory Fleet will loose as predicted, and the ground forces on Earth will be slaughtered (which is pretty morale breaking for everyone else). Also, even assuming all of this is a dream and the Indoctrination fails, what then? Shepard is lying unconscious on the ground, as soon as they realize the Indoctrination failed the Reapers are going to do what they did 99.9% of the rest of the time -- he's going to get blasted to death and then everyone dies.
Shepard is unneeded. The failed assault was the organics last throw, if it fails they are done for. Their morale will break from having their one and only plan fail along with the death of the bulk of their remaining military forces. They also don't need Shepard in a thinking capacity. He only has to perform menial tasks -- hell they could probably even rig him with animatronics and puppet him, no one would know and it would accomplish the same thing; namely that Shepard would appear to be working for the Reapers now after they already won.
Also -- and this is probably the most important part -- the Indoctrination that supposedly happens in IT isn't anything at all like the Indoctrination in the story, it's something completely new. Indoctrination isn't trying to break someone's will, it's electromagnetic waves that physically damage a part of the brain -- you can't resist Indoctrination. It's even been one of the major themes of all the Indoctrinated characters' arcs that all the antagonist are strong willed people who succumbed to Indoctrination, showing how truly awful a method it was for subverting organics."
While that is true, what I believe happens is that in the ultimate Destroy ending, you have enough assets to distract the Reapers from blowing up Shepard. It makes sense how the only way to stop Harbinger from finishing off Shepard would be either the Normandy, Some sword fleet, or Anderson with Hammer team/Shepard's squadmates, past and present take on Harbinger in order to allow an extraction team find Shepard and take him/her back to their new base.
That is true. However Shepard in the records in the time capsules would inspire the other organics, and synthetics in the next cycle. It is most likely how the Reapers used the collectors( Protheans) from the last cycle, Shepard would be used as a guide to the next cycles destruction. They could have Shepard be put into a pod and when the time comes either the Reapers open the pod, or an organic or synthetic science team finds Shepard's pod. After all we did find Javik's pod, so it is possible the Reapers would have more use in the next cycle. Not to mention we still don't know if anyone could have made it from the battle at Earth. Hacket, some of our squadmates, and some parts of hammer and sword could have escaped to continue to make some small hint and runs, causing the cycle to go on for another 50 years at best or maybe more. Javik's people fought the Reapers for century. It could take that long.
Not true. Zhu's hope knows they are being Indoctrinated yet their time with the Thorian caused them to link minds to one another and not feel the affect's of Indoctrination. My guess is Shepard will mind link to Leviathan at best if you have the dlc, the Rachni queen if you saved her in ME1, or possible Liara.
Now though it could be a new form of Indoctrination, IT still holds up because even though it could be a new form of Indoctrination, Shepard experiences a good portion of the symptom's of Indoctrination taking place. Not to mention we know that Leviathans have a earlier version of Indoctrination, and the reapers perfected it more, it is possible that the Reapers can not Indoctrinate Shepard their old way, so they must have Shepard willingly give him/herself over to the Reapers. ( Control and Synthesis). Yet Destroy is not handing the Reapers what they want. It is instead, Shepard is sticking with the mission at hand, and regaining part's of him/herself that the Reapers tried very hard to suppress. That is just my take on it though, I don't want anyone to think that what i could say speaks for all supporters of IT, and theorist.