And to just repost why I don't like indoctrination theory is:
I really don't like the implications of the indoctrination theory for several reasons. If I just excluded the fact the no one can release themselves from indoctrination for a moment its bad in the sense that shep is still in the ruble and dying! That means it was a dream before he wakes up in said situation he is either
(A) Now too hurt to continue to stop the reapers or
(

has to drag his ass to the beam again to do exactly the same thing he did before with minus the whole shooting Anderson and starchild events.
Both mean shep has lost valuable time his fleets both on ground and in space are getting more and more thinned out while he's laying there which means by the time we get to whatever it is that truly controlled the crucible in the first place we would've lost 50 - 80% of our troops so while we're there racking our brains to figure out how to turn on the crucible (considering it will turn on in reality now) by the time we get around to destroying, loving, cooperating with the reapers our troops aren’t' going to fair well and sheps probably still going to bleed to death before he can either (A) have a doctor get up through the beam to get him or (

drag his ass back to the exit point and that's being generous thinking the beam works both ways and infact won't be shut down as a result of shep's choice to love, destroy, or cooperate with the reapers.
Now back to the indoctrination breaking free problem; YOU CAN'T DO IT! Benezia, TIM, Saren, Feros girl, and other couldn't do it.
But wait TIM only got hit by a beacon and lived! But he also plugged into his brain the whatever he used on sanctuary to turn people into husks he is now a more advanced husk but still indoctrinated.
But shep hasn't been exposed to enough reaper tech! Yes he has:
1. the beacons based off of reaper tech
2. Rho for 2 days sedated within the base within range of the reaper waves how do I know this? The staff in that area complain about it! Also a sleeping at rest mind will accept lies, propaganda, and other brainwashing techniques easily and without question so shep could've gotten up to a weeks worth of waves and influence done in just 2 day
3 EDI has reaper tech in her Shep may also have reaper tech in him this could be benign it could also indoctrinate until the LP files are known this is a wild card
4. The geth world he was plugged into the same system as reaper code was this could also imprint itself onto him
5. Out cold next to Harbi we know reapers admit waves sense ME he could've always broadcasted that while shep laid there his mind yet again accepting anything Harbi told him as truth.
We first meet Benezia who states that no matter how strong the mind or the will given long enough exposure to a reaper's influence you too will become a thrawl like her. She broke out of its hold for 3 minuets before she was overcome.
6. Shaila (the consort) walk around there listen to the people, her people! They feel called to come back to work for her, every member there is in a spell over her, they can't put their finger on why she's everything to everyone they just don't know it yet. To me this girl screams reaper thrawl and a willing one at that if you melded with this girl you've got two thrawl melds and potential reaper corruption!
Saren: Questioned his programming but in the end was retrofitted like shep and even though a part of him knew what was happening more of him wanted to just keep doing what the reapers said and in the end if you make him kill himself they just take over his tech anyway.
Feros girl: Became a thrawl along side Benezia then was given to the plant she now claims still to feel the plants influence over her connecting her to her gang of colonist but also to hear the reapers signals and feel them calling her. She says the only way she's fighting them off is to live beside her colonist and they must stay as a hive minds otherwise they will answer the reapers calls.
We have many other examples during ME of indoctrination some knew it was happening but once that epiphany struck they still couldn't do much to stop them from turning.
The end result was known via vigil once the reapers leave a system the thrawls can no longer function they become mindless and no longer have a self preservation instinct.
So this suggest only a few loop holes for an indoctrinated shep who is only semi broken the hold of Harbi he'll become a mindless thrawl once he chooses to destroy the reapers, or if you can keep a constant power source running on a reaper artifact he can live within the area it is housed and no one else can because they would be indoctrinated he must stay near the item to literally keep functioning.
So the indoctrination theory ends way worse then any confusing ending of the Normandy crashing ever could you will not get a happy ending out of this other then shep's alive unless BW wishes to override and retconn how they've established for 3 games how indoctrination actually works all because its shep and when shep is involved all lore, law, and physics can go out the window.
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And if it's a dream shep is having after he got cooked by Harbi's laser then:
(A) Now too hurt to continue to stop the reapers or

has to drag his ass to the beam again to do exactly the same thing he did before with minus the whole shooting Anderson and starchild events.
Both mean shep has lost valuable time his fleets both on ground and in space are getting more and more thinned out while he's laying there which means by the time we get to whatever it is that truly controlled the crucible in the first place we would've lost 50 - 80% of our troops so while we're there racking our brains to figure out how to turn on the crucible (considering it will turn on in reality now) by the time we get around to destroying, loving, cooperating with the reapers our troops aren’t' going to fair well and sheps probably still going to bleed to death before he can either
(A) have a doctor get up through the beam to get him or
(

drag his ass back to the exit point and that's being generous thinking the beam works both ways and infact won't be shut down as a result of shep's choice to love, destroy, or cooperate with the reapers.