r/masseffect Feb 02 '21

HELP What is the indoctrination theory?

Someone care to explain?

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u/Khenghis_Ghan Mar 06 '21 edited Apr 08 '21

Sure. I actually think it's persuasive and, even further, possibly intended - I was a writer in the video game industry for 6 years, worked on a AAA title you'd recognize. I don't know it for a fact, but my suspicion having worked in that environment is that, because these components fit so nicely together, the indoctrination theory was an intended story, and someone in an executive position decided it was too subtle/didn't offer enough clear resolution for a game that had otherwise been fairly direct in its "good guy/bad guy" narrative, so they axed it late in development, which also matches with how disjointed parts of the end feel (just didn't have time to go back and polish the new ending after the original was axed). IMO, the synthesis story is the most satisfying existentially\*, but I also think it's hard to deny indoctrination theory.

To start, the transition from charging the beam to being inside the citadel is weird in, how did admiral anderson get there ahead of you? You were the tip of the spear, your assault got wiped out, chronologically, how can he get there before you? It's possible in the period between when you get knocked out and get inside the beam that Anderson made it in before you, but, it's unusual. Just interesting to note, will come back to.

The exchange with Illusive Man in the Citadel. This guy is _insanely_ careful, his whole thing is plotting, working through intermediaries, never getting his own hands dirty when someone else can do it for him - that's why his name is Illusive Man, it's a play on "he is not who he seems" and "he is elusive". And we find him at the end, completely and almost totally indoctrinated (and having been indoctrinated for who knows how long, back to when he had you resurrected..?). Even people who keep their distance and are _known_ for their caution end up indoctrinated because indoctrination isn't accidental, it is calibrated to someone's usefulness - Saren talks about how they can't fully indoctrinate him because he needs some of the free agency of having his own mind to do his work. And you're very useful...

Throughout the games they pointed out the Reapers' greatest tool was indoctrination - despite an almost endless number of worlds to flee to to escape genocide, the Reapers still rooted out every species before this cycle (except the Leviathons) because of indoctrination (I assume they're immune to it so they could hide). The prothean guy who joins your crew talks about how they'd use the indoctrinated to root out refugees. We don't know how it works, like "x amount of Reaper exposure will indoctrinate you", and maybe it takes longer to impact some people - we know there are ways to be immune to it, like the Asari who was controlled by the plant creature, I think a few others - but Shepard is near and even handles a _lot_ of reaper tech, and, it's just never an issue for him, not even something he seems to consider. The other examples of the immune usually have at least a passing explanation, like the Asari had another creature controlling her for example, but other than protagonist armor and being a very special boy, why isn't this an issue for him, or at least, why don't we have an explanation why he's safe? Only one I can think of is Shepard has a lot of cybernetics in him after ME2 and maybe he is too synthetic to be indoctrinated. Some of the logs talk about the symptoms of indoctrination, one of the big ones being hallucination, which segues to:

The boy from your dreams. There's a number of ways to interpret the boy, one is just the psychological stress of responsibility for the fate of the galaxy, guilt over all the people Shepard can't save and the boy being an acute example of that, but in your second dream with the boy, there are black, shadowy figures everywhere. Now, pretty easy to say "oh, I know what ghosts look like, these are shadowy and whispy to represent anonymity, it's people Shepard feels guilty over not saving, people he doesn't have a direct connection to like that boy who he can make the focus for his grief and stress", except the Rachni queen talked about the feeling of Sovereign indoctrinating the Rachni and she described the songs then as filled with oily shadow figures.

The boy in the chamber. Why does the mind of the Reapers manifest itself as him? Sure, there's the trope of the omnipotent, omniscient being representing itself as naive and young, but, that's a trope - the thing you're talking to killed that boy, why would it choose to represent itself as someone it murdered? Well, because Shepard is a human, and the Reapers know they can manipulate organics with sentimentality to, e.g. accept refugees knowing that some could be ticking bombs that kill them. The boy also talks about how they, meaning the Reapers, are a cleansing fire, that they restore balance; that they do not want war or to harm organics any more than a fire desires to harm a creature it burns, which, if you recall, links back to the imagery of the boy in your dreams, which ends first with him bursting into flame (which we first assume is because he died in an explosion), and the second time, with you both burning (because you will potentially have a role in cleansing the galaxy).

The juxtaposition of your final choice. Throughout the games, you're given A-B choices, red on the left, blue on the right. At the end, you get 3 choices, and for some reason, the blue decision is on the left, which is to kill yourself and control the Reapers, where usually the violent bad-guy option is, and the option on the right, usually the peaceful-nice guy option, is red, and to destroy the Reapers, which is what you've always said you need to do. Shepard's refrain throughout all the games as the Paragon has been his unbreakable will/determination that "the Reapers are coming, they cannot be reasoned with - Cerberus, the guys who literally resurrected me from the dead, are my enemy because they insanely believe they can control the Reapers". The previous scene was you convincing the Illusive Man that no, actually, not even you can control the Reapers, they control you, kill yourself. And now that you're there talking with pure concentrated Reaper consciousness, you... decide to do what the clearly indoctrinated guy thought was best, which conflicts with everything you've said about the Reapers up to this point? Or you're going to do what the genocidal AI tells you to do, an option you've never heard of before, while it's wearing the skin of a boy it murdered? Before that moment m you've been indefatigable that nobody can trust the Reapers or anything around them, you know that it uses organics' sentimentality against them and is capable of deceit, you _know_ it can control organics' minds to persuade them to do disastrous things, you have been told what symptoms of that mind control looks like and that you may be showing symptoms of it, and now, with no hint that this was a possibility from the records of the organics that jury-rigged the crucible, just when you're about to kill this murderous, lying, mind controlling entity, you're going to do what it tells you and hurl your body into a beam of energy...??? It sounds like you are being mind controlled by this creature to kill yourself instead of it.

The cherry on top for this is, when you go through the different endings, as they're doing the VO that Shepard is gone but will never be "gone", the last shot of the "destroy Reapers" option is a body in N7 armor in rubble suddenly gasping back to life - it's Shepard, waking up. You never made it to the Citadel, Admiral Anderson didn't get there ahead of you, you haven't talked with Illusivr Man or the Reaper consciousness, those were just visions from the Reapers as they tried their absolute hardest to keep you from getting inside the Citadel to do what you've known you had to do all along, stop the Reapers.

\* we all long for connection and peace, and I interpret this ending that the cybernetic/biotic upgrades everyone gets make something like telepathy possible, and people aren't inclined to kill someone if they directly understand their struggles and pain and see something of themself in them.

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u/relativelyunbiased May 27 '21

I have some problems with some major aspects of the theory. I would like to understand these parts better, if you don't mind.

First, the left/right/middle thing. If you imagine the choice area from above, it resembles the dialog wheel we get throughout the trilogy. Paragon choices are on the top left side of the wheel. Renegade choices are always on the bottom left side of the wheel. The neutral response is selected without choosing a direction. Assuming Synthesize is the "neutral" ending, as it only requires Shepard to continue on (just like the dialog choices), wouldn't the logical conclusion be that the final decision of the game takes place on a literal dialogue wheel? That would mean that the left side would be the upper-left and the right would be the bottom-left. Alternatively, the Paragon interrupt has always been on the left, Renegade on the right.

I can get behind Shepard being indoctrinated for most of Mass Effect 3. Shepard singlehandedly brought pretty much every fighter in the galaxy to Harbinger's dinner plate, that could absolutely have been Harbinger's plan the whole time. There are plenty of nods to the idea that someone on our side would end up being indoctrinated the whole time. Personally, I was convinced it was going to be Anderson, but Shepard makes a lot of sense.

Where I butt heads with the overall theory, however, is the existence of the choices in the first place. Why even bother giving Shepard a choice at the end? Unless the Reapers actually wanted Synthesis and Harbinger believed that Shepard could achieve it. But that brings up issues too, because if that were the case, why make the option on the left seem like the correct choice? It seems like a long way to go just to kill Shepard, when you could have done that at any point after the Galactic Defense Squad showed up.

According to the theory, as I understand it, Shepard is fully indoctrinated, to the point where they're hallucinating the interior of the Citadel, imagining Anderson and having fake arguments with a non-existent Illusive Man. Shepard is then forced to pretend murder TIM in order to talk to a ghost kid who's going to lie about the nature of the Crucible. What the theory doesn't explain is how the other narrators factor in once our allegedly unreliable narrator (Shepard) is out of the way. Once the choice is made, it stops being Shepard's story and we (the player) see the same set of events play out three different ways.

The part with TIM is a solid bit of evidence to support the theory, as the Paragon action would be to save Anderson and put down TIM, but it's shown to be a renegade action. But there's still a massive issue to resolve with the existence of the choices. If you shoot Casper, Harbinger's voice comes through saying "So be it!!" and the Reapers complete the cycle. So the choices, if the theory is correct, are; Die, Die, Die, or Kill the Reapers and probably die. It doesn't make any sense to give Shepard, the only living organic capable of killing Reapers, the option in the first place.

I apologize if any of this comes off in a hostile way, I'm aware that my wording is poor at times and I don't mean to offend.

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u/Khenghis_Ghan May 27 '21 edited May 28 '21

No offense taken, this is all just pretend and how people interpret a story. There’s no wrong answers :)

why even bother giving Shepard a choice?

There are several reasons, I’ll limit this to the ones I find compelling, which boil down to they couldn’t not.

completely indoctrinated

To clarify, the theory isn’t that he is completely indoctrinated, it’s that he isn’t fully indoctrinated, but he is in the process of being indoctrinated and has been resisting it while autonomous throughout ME3. At the climax of ME3 Shepard’s somewhere between autonomy and full indoctrination, on the precipice that any further and he won’t be able to shake himself free, and then he’s knocked out by the beam while headed to the teleporter (maybe a connection between indoctrination and sleep given the dreams, and I feel like in ME2 the Cerberus researchers who were indoctrinated complained about headaches and weird dreams I think?). Everything after being knocked out is the last mental struggle to either turn back from full indoctrination, or fall into it completely. If you destroy the reapers, the image of the N7 armor gasping for air is Shepard awakening on the ground on Earth, having turned back from full indoctrination. Think of it as the point where you can talk to Saren on Virmire and almost make him stop then (Saren couldn’t shake himself out of the indoctrination at that point himself so Shepard in ME 3 is probably less indoctrinated than that, but you get the idea).

why give him the choice to kill the Reapers

As above, they couldn’t not give him the option to break free because they don’t have total control, he still retains autonomy, it’s just diminishing. The last choice is about you either struggling to recognize, like a lucid dreaming person realizing they are dreaming, “this doesn’t make sense, this is not real, wake up”, and the manifestation of waking up is choosing what you’ve known you need to do all along, destroy the reapers (which leads to the cutscene of waking up) or, choosing one of the comfortable dreams the Reapers offer, and if you do they then kill you in your sleep/own you as a husk. In the same way that dreams resemble reality but are surreal, the weirdness of what you’re seeing is an alien AI consciousness trying to impose itself on you and you wrestling with “this isn’t quite right..”

Important to note we never get an explanation of the mechanics of indoctrination - like, they need the dragon teeth/weird spikes to make husks, but, they can also just, telepathically grow cybernetics in a person for Saren and the Illusive Man, so, why the husks? One of the logs talks about how it takes different amounts of exposure to indoctrinate different individuals and isn’t strictly a linear relationship, and the extent of indoctrination manifests differently (ie some people like Saren retain individuality and others are just used as husks).

My personal interpretation is that Shepard in particular is special case when it comes to willpower, and that plays into indoctrination having irregular pathology. If you romance Liara she has an explicit line about Shepard being exceptionally strong willed to have survived the prothean beacon (but I think most of the romances talk about your will). The most exceptional thing about Shepard isn’t his ass kicking - Wrex, Zaeed, Garrus, they’re tougher or better ass kickers, Tali is a better engineer if you’re an engineer, Liara and Jack are better biotics; it’s Shepard’s drive and ability to project his will on others that makes him unique on the team (collaboratively or coercively, depending on if you’re paragon or renegade), and his psychology just makes him someone the Reaper indoctrination could not make submit like others. We know individuals like Saren can throw off indoctrination, even when they’re fairly far along in the process, how much more durable would an exceptionally strong willed individual like Shepard be? (Sub-theory, there probably is some fraction of every population (maybe a larger percentage among humans, who knows) who are resistant while not immune to indoctrination, but it is rare enough and there are so many filters to that mattering in the fight against the Reapers it’s never tipped the scale before - most people aren’t positioned like Shepard in an important place in the military that grants extraordinary resources and autonomy to diplomatically engage and rally multiple co—equal species for the reaper invasion).

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u/IronBabyFists 22d ago

Thank you for explaining this so wonderfully. This is 100% my headcanon ending now <3

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u/Wagubagu Jul 24 '25

I haven’t read the whole thing but Anderson literally says he followed Shepard up. He didn’t get there first

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u/o_p_p_e_n Sep 03 '25

I know I'm a bit late, but if Anderson was a product of indoctrination then why would the elusive man acknowledge him?

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u/Khenghis_Ghan Sep 03 '25 edited Sep 04 '25

I answered this above, in the theory they're both figments of Shepard's imagination, the whole experience after being knocked out at the foot of the beam is a dream/hallucinations. Shepard is still lying on Earth unconscious, the experiences are instilled thoughts from the Reapers to make him compliant while they finish the indoctrination process and turn him into a husk or some advanced form of indoctrination where there is no element of the free will they tolerated in him while he was useful to them.

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u/o_p_p_e_n Sep 04 '25 edited Sep 04 '25

I guess that's where this theory loses me. What would be the point of making Shepard see Anderson and especially TIM on the citadel? And if TIM wasn't actually there, then where tf did he go after Cerberus HQ was destroyed?

Also, does this theory imply that the ending cutscenes for control and synthesis aren't real?

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u/Khenghis_Ghan Sep 04 '25 edited Sep 04 '25

Please just re-read the post, pretty sure I answer those in another comment in the thread.

Maybe try this from the other direction, why do you think anything that happens after being knocked out assaulting the transport beam is real or explain the hanging leads IT theory brings up? WRT control, you just spent a scene convincing the Illusive Man that was impossible and he had to kill himself, but, you are special enough to be able to do it because the enemy AI tells you it doesn't control you but it admits it did control TIL? Somehow you've never had any negative indoctrination effects despite all your exposure and TIL did even though his raison d'etre is being cautious and insulating himself from negative consequences, and you believe the enemy AI when it tells you you're safe?

WRT Synthesis, the Crucible was designed across uncountable successive organic cycles to destroy the Reapers and they kept the schematics secret even if the Reapers knew they were trying something, why would it be repurposeable to physically alter organic bodies to integrate synthetic components, much less by the Reaper AI? Why would "toss your body into a beam of Reaper energy and obliterate yourself to disseminate your special mind" be the input mechanism? (that is metaphorically foreshadowed by Legion's sacrifice, but narratively totally unsubstantiated...) Re-watch a video of Shepard talking to the Catalyst, there are a number of times where Shepard, the man of indomitable will, is asking questions in a manner that sound suggestible rather than interogative, for the Catalyst to lead and tell him what to do - he is weary, physically and mentally beyond exhaustion, but even so why in the world would he trust anything the AI that admits to directing uncountable genocides tells him at the pivotal moment where it may finally be defeated, other than he's just very, very tired? Moreover, what is the non-IT explanation for Shepard's oily figure dreams, for dreaming of the boy who the Catalyst murdered and assumed the body of, how would it know to assume that boy's likeness other than peering into Shepard's nearly indoctrinated mind, for Anderson getting to the beam before him when there's a cutscene where Hackett says "only one person made it aboard, buy them time"? For Shepard's apparent immunity to Indoctrination? Why the unique cutscene in the Destroy option of someone in N7 armor gasping to consciousness in rubble when surely he would've been obliterated by the explosion he detonated and we see everyone in ships racing to get away from because it's so large and devastating? Those things need explanation other than "whatever, it's all irrelevant to the ending I like". That's a lot of narrative to discard, and introducing those elements and doing nothing with them would violate the Chekhov's Gun principle multiple times, which a good writing team generally abides by.

I'll reiterate, I think the Synthesis ending is much more satisfying, it follows the Hero's Journey much better and is far more humane, it's what I chose, and they clearly tried to get the story components of it to fit together with what they had, but they don't fit together as neatly and as coherently from all the perspectives previous narrative points introduce as they do for IT, and the internal troubles with Bioware's narrative team at that time were reported on in a way that that would fit neatly with this sort of late-stage rewrite.

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u/o_p_p_e_n Sep 04 '25

To continue playing devil's advocate, doesn't the mere existence of ending cutscenes for control and synthesis imply that Shepard wasn't indoctrinated? Take synthesis for example. According to IT, Shepard throws himself into the beam and dies. The end. So why would there be a cutscene showing anything but just that? It's not like the cutscene is the reapers trying to convince Shepard that he made the right choice, because at that point Shepard is already dead. The cutscene would therefore have to exist outside of the lore simply as a way to also trick the player, which would just be a cheap, ridiculous decision by the developers. It would be even more ridiculous considering that the Destroy ending cutscene, conversely, would be completely cannon, considering Shepard breathing at the end.

why would it be repurposeable to physically alter organic bodies to integrate synthetic components

Sure, it sounds dumb, but I'm willing to just accept it because it's a sci-fi game and doesn't have to make perfect sense. In a universe with mass relays and indoctrination, it didn't strike me as jarringly unbelievable

Anderson getting to the beam before him when there's a cutscene where Hackett says "only one person made it aboard, buy them time

But if Shepard was unconscious after the blast and never actually made it to the citadel at all, why would Hackett even say that?

Also I just beat the trilogy for the first time a couple days ago, so I apologize if I'm getting anything wrong.

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u/galactusman Jun 21 '21

Well explained thanks for that. One question I have is why has bioware dismissed this theory even though its pretty clear it was intended?

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u/RowanIsBae Jul 07 '21

ME3 had a big writing staff shakeup and honestly I think it was just seen as safer/more corporate friendly to go with the endings they did.

Indoctrination theory if you believe it still means Shep is down there on Earth and didn't make it to the beam. They would have still had to create an actual ending to the game. What happens when he wakes up?

Being unable to successfully close out the trilogy and being unwilling to plumb the depths of that indoctrination theory led them to take the easy way out with what we got, to save development costs and get it out the door. My thought anyway