I posted the following on Forbes, to good reception:
The theory does not assume Shepard IS indoctrinated. The
process takes sometimes a long period of time (if the rate of
indoctrination is slow enough, sometimes months), and it only seems to
have long term effects if the organic actually submits to them. Saren
started off as an indoctrinated tool (given enough control over himself
to do his job and continue to research the Reapers), but his process was
also over months and he had opportunity to reject it… until he
basically stationed himself in an actual Reaper.
Basically, there are different ‘stages’ to keep into account:
1)Beginnings. Some visions, whispers, and maybe a little more foggy mind, more sense of depression etc.
Subject = redeemable, but get him away from anything Reaper related!
Shepard = according to theory, he’s in this stage since at least
Arrival. He is, however, perfectly capable despite that, and his choices
are still 100% against the Reapers. Reminds me of Frodo, who had dark
moods and despair even after Sauron was defeated.
2)Illusion = The illusions get more vivid, to the point of
misdirecting your actions and beginning to change your philosophy.
Greyson in the novels reaches this point, but is only tipped over the
edge by Cerberus giving him Red Sand to compromise his mind. Saren was
kept around this stage for quite a while before ME1, and it seems in
ME3, TIM also heads into this stage. Benezia also likely held onto here
for a while, until she became overwhelmed by being on an actual Reaper.
Subject = mostly irredeemable, with exceptions. The subject may be still
useful and might fight against the Reapers, but the ‘dark tendrils’
very strongly influence the mind. The Rachni queen in ME3 (if you saved
the ME1 one) may also be at this stage, but more capable at rejecting it
than a human would.
Shepard = He’s at this stage by the time he gets to Earth in the end.
Getting hit by the blast only tips him over, into his own ‘crucible’ to
decide whether he will fight off the indoctrination, or fall into it.
Thessia, and the defeat there, seems to be the tipping point into this
stage, and direct Reaper presence (hello Earth) is all that’s needed to
push him over.
Conversion = The character now believes in something else, just
anything BUT destroying the Reapers. The more paragon minded might
believe that working with the Reapers or alongside them, is realistic.
The more Renegade minded might believe that controlling them or at least
using their technology in dangerous ways, is realistic. Overall, the
slide into become a slave is now clear to the more lucid minded. Saren
is this throughout ME1, until his near total conversion at the Citadel.
Benezia is as well, but she (with her biotic-magic-meditation-stuff) was
able to lock out a part of her mind to the indoctrination. TIM is
likely strongly into this stage in ME3, and his implants only tip him
over strongly.
Subject = irredeemable, seemingly. People like Shepard CAN break through
to them though, but only for a short period of time. The subject will
likely opt for suicide at this point, if anything. Samara’s daughter
also opted for setting off the bomb, instead of going with the others,
because she knew she was lost.
Shepard = only at this stage if Synthesis or Control are chosen. You’ve
already ‘lost’ then. I’d love if alternate endings happen with these,
but they would be ‘bad’ endings (at least resulting in Shepard’s death,
maybe suicide if your squadmates have strong relationships with you and
can talk you down).
Thrall = Now fully in the Reaper’s grasp, the individual is so
different from his normal self, that anyone can see it from a mile away.
This is the eventual result of the Reaper’s indoctrination by itself,
and the Reapers tend to hold back on it for their more useful sleeper
agents. Regular guys though? They’re screwed, and left to worshipping
the Reapers with gibberish.
Subject = shoot him, he’s lost. Maybe, in better conditions, could be
put into a psych ward. He’s not useful to you, nor the Reapers (unless
they are huskified), except as crazy suicide bombers or something.
Shepard = Not here at all! The Reapers likely don’t even want him to
become this, or even a Saren. They’d likely want him to be secretly
under their thumb, so he can lead the entire galaxy to their doom.
Husk = by which, I mean a husk of the former self. This can mean
literal husks (aka total puppets), or organic slaves (like the
Collectors). In any case, there is no free will left, and the subject
exists only for the Reaper’s more ‘manpower’ required goals, like
infantry, or large scale projects like construction.
Basically, the BIG point on whether someone is ‘being
indoctrinated’ and actually ‘is indoctrinated’, is the space between
Illusion and Conversion. A surivivor of Illusion may just end up with
long-term PTSD, but once into Conversion, you’re already dead inside.
~~~~~
And there can still be 3 endings.
Control = the first major stage of indoctrination in strong-willed
individuals, convincing them that they can actually control the Reapers.
Illusive Man is currently in that stage (even if you discount the TIM
you meet in the supposed ‘dream’), but even Saren initially believed
that by boarding the Reaper and studying it (Virmire), he’d be able to
learn how to control them. This transitioned into..
Synthesis = the last major stage of indoctrination in strong-willed
individuals, as it embodies co-operation and the start of the idea of
subserviance towards the Reapers. It’s fairly bright at first (we’re all
going to be together, organics and synthetics!), but turns into a hope
that you’ll be spared from Reaping if you accept synthesis, and then
eventually into an outright worship of the Reapers. Saren lasted until
this stage, but if it went any further, he would have been an outright
slave like Amanda Kenson. Kenson started by wanting to destroy the
Reapers, but transitioned towards worship and then becoming a slave, as
her mind never throught of controlling of co-existing with them, but
stronger-willed individuals may go through a slower process.
Destroy = the goal all along. Every points to Shepard and Anderson
showing the Reapers no way into their minds. Shepard rejects Saren’s
Synthesis, and TIM’s decline into Control philosophy.
And each can still have their own endings.. its just that 2/3 would
lead towards bad endings. And to by honest, plenty of people wanted bad
endings, just as much as they wanted to be able to access the ‘happy
happy joy joy’ types of endings.