Indoctrination Theory Confirmed: Or, How I learned to Relax and Love the BioWare

I’m a latecomer, I know. I’ve been clinging to pieces of the indoctrination theory because it was the only thing that I felt could POSSIBLY excuse, let alone explain that monster of an ending.

Yes, THAT monster of an ending. Wait, no, this isn't the monstrous part. Spoilers follow, obviously.

And the more I think about it, the more everything fits. It just… takes getting used to.

I’ve seen lengthy analysis on both sides, weighed the arguments, and finally been pointed to the one last piece of evidence that I feel constitutes proof that something is legitimately weird here, and that BioWare did it on purpose. And suddenly, I realized I’ve been maddened because I’m not used to treating games the way I treat movies. But the non-interactive nature of the ending… sort of demands that treatment.

And if so… then the ending to Mass Effect 3 may well be the most legitimately amazing thing in the history of video games, and I am merely disappointed that the story seemingly ends before the best part — something I now hope will be corrected in the Extended Cut.

Before I continue, though, I will also add: I still stand with RetakeMassEffect and HoldTheLine.Com – and I refuse, categorically, to accuse anyone of disliking the ending because they ‘don’t understand it.’ Simply put: there are multiple levels to view any piece of fiction on, and this is a BIG jump to make in a series like Mass Effect. One that has never before asked us to question Shepard’s perception of reality, or our own sanity. Viewed on a surface reading, the ending makes no sense and is objectively terrible, violating many of the series primary themes and possibly condoning genocide. But I write this because I now dare to hope that there’s something behind that surface, something that is begging us to look deeper and question what we are being shown. I write because I am convinced that BioWare took a huge storytelling risk… and is now watching it backfire spectacularly, and handling it the best they can.

Indoctrination Theorists: I beg you, let the theory stand on its own merits. Present your evidence to all you wish, but accusing people of being “too linear” or “not understanding” does you no favors. In short, don’t be a dick.

Let me run through what convinced me, and see if it will do the same for you. I’ll start with the common evidence and move on from there.

1. Shepard’s dreams.

First of all, these dreams (like much of the ending) are barely interactive. There’s only one thing to do: move toward the kid, hear whispers, see shadows, hear reaper noise, watch kid burn.

We hate this child. Seriously.

I won't lie. You go through this dream sequence enough times, pretty soon you start to cheer when the kid bursts into flames. This game gave us ISSUES, man.

Shepard has three of these dreams, getting gradually worse (more shadows, more whispers from dead friends, all that rot), but they’re all basically the same except for the last one. In the final dream, Shepard sees himself embracing the child, then watches both of them burn. Not happy, nor frightened, just staring at him. And since we’re talking about character models and not actors… we have to conclude that those expressions are very deliberate (Meanwhile the look on Shepard proper’s face is much more in tune with the nightmarish nature of the scene).

Side note: it could be argued that scenes like this are where Mass Effect 3 feels the weakest, and also the least like a video game. But that would be an entirely separate issue, and since Batman: Arkham Asylum/City both did it and got away with it, I’m willing to let it slide. Let’s move on.

The first two could be mere nightmares, Shepard mourning the loss of those he couldn’t save, but this one is different. It has a distinct meaning. And given the ham-fisted symbolism here it’s hard to read it more than one way.

The obvious interpretation: embrace the child at your peril. Following this child will lead to your doom, Shepard. Take heed. This is a warning.

This, however, is just true. And a little funny.

2. The trees.

Shepard’s “unhappy place,” as I like to think of it, has very distinctive trees. These appear again as Shepard sloooooowly staggers forward toward the teleport ray (and a possible death at the hands of Marauder Shields…) after Harbinger’s beam, but not before. They had to be added deliberately.

Seriously. THOSE WERE NOT THERE. There has to be a reason for that.

One could argue that they’re simply reused art assets, but one would still have to contend with the fact that they weren’t there before Shepard was struck. Why add them unless something has changed?

Either Shepard is unconscious and dreaming, (fairly likely given the other logical inconsistencies that have been well covered by many others, such as Hackett’s radio call), or she is conscious, but hallucinating. A LOT. And lest we forget, the second game spent a LOT of time hammering home the idea that Harbinger wants Shepard alive. And right now, Shepard is right where the reapers want her.

3. Shepard’s wound.

Putting aside the questions of the pathway – how Anderson got here first, how he followed us up when there’s only one path, where The Illusive Man even comes from, why there’s still TRAFFIC on the citadel when it’s been cleared out by the Reapers… Ignoring all of that, even though it’s reasonably compelling on its own. Putting aside the question of how The Illusive Man could control Shepard without a control chip (something the game reminds you you don’t have several times, very deliberately – the plot point gets like three subplots devoted to it).

We also spend a lot of time looking at this face, which now not even a mother could love. But that isn't important yet. Keep reading.

Shepard is forced to shoot Anderson in his lower left side… then shown shortly after clutching that spot on his own side, bleeding from a fresh wound. Don’t ask for a picture here: YouTube it if you want to double check me. It’s easy to spot.

That does not happen by accident. We are shown this very deliberately. We are meant to see it and question it and think about it. It gets its own close-up, and as an old girlfriend once told me, close-ups tell the story. A close-up only happens if the filmmaker (or game designer) wants to draw your attention to a detail.

In any film, this would be an obvious sign… and since the game is at its most film-like here (annoyingly enough: separate issue entirely, as I mentioned above) we have little choice but to interpret it the same way we would in a film. Conclusion? Something is rotten in the state of Denmark.

4. The sudden reversal.

Oh, HAI there, creepy child from my nightmares! I instantly believe everything you say, because I find the word of a genocidal monster that preys on my subconscious implicitly trustworthy! I'll just shuffle toward my doom, now.

Suddenly, we are lifted from a setting with a few inconsistencies (but still mostly believable) to a world of seemingly utter nonsense. If taken at face value, this scene raises more questions than I can count, and the only conclusion I can draw is that it was meant to. For example?

  • Why does the AI look like the child from my dreams when I’m the only one who knows what the damn kid looks like?
  • Why am I shooting this tube?
  • Who designed this crazy thing?
  • Why didn’t they just make a big red threatening button and put a sign over it that tells me, “please don’t touch that?”
  • Why can’t I argue?
  • Why do two of the options presented – the ones this child claims are optimal – sound so incredibly STUPID?
  • Why are we suddenly pretending that controlling the reapers is a paragon action when I’ve always paragon argued against it?
  • What the HELL, space magic?!?!!?1!?!ELEVEN?1!?

And so on.

Mass Effect does not deal in “transcendent planes of existence,” – never has, probably never will, and if it was going to it damn well should have foreshadowed it somehow – so anything this illogical can only be a) completely real, poorly written, and therefore a giant waste of my time and money, or b) completely unreal, and a construct of Shepard’s mind.

It only makes sense if interpreted as a fundamentally unreal experience… and it only makes sense if you understand Indoctrination and are familiar with the two previous major villains of the series, Saren and the Illusive Man… One of whom you were reminded about when you watched him die, indoctrinated, not two minutes ago, and the other of whom you MAY have been reminded of at the same time when The Illusive Man shoots himself – just like Saren.

Side note, Saren and the Geth would be an AWESOME Mass Effect themed band.

Yes, THAT Saren.

(Unless you’re like me and you just shot TIM yourself. And who can blame you?)

The AI offers you three paths, two of which it claims are better. Control and Synthesis. Control is advocated by The Illusive Man, Anderson (who has always been someone you trust and agree with) stands for Destruction… And Synthesis was advocated by Saren in the first game. Don’t believe me? Try this quote on for size:

I’m not doing this for myself. Don’t you see, Sovreign will succeed. It is inevitable. My way is the only way any of us will survive. I’m forging an alliance between us and the Reapers, between organics and machines, and in doing so, I will save more lives than have ever existed. But you would undo my work. You would doom our entire civilization to complete annihilation, and for that, you must die.

You, the player, are meant to remember this detail and question this. Shepard cannot. There is no other logical explanation for a reversal of this magnitude.

And lest we forget, I refer you back to Shepard’s dream. Siding with the child leads to her doom.

Proof? I can offer proof.

5. The music, and the final visual cue.

Sadly, these two last warnings do not appear until it is too late to change your mind. And had I not sought video of the two endings I didn’t choose, I might never have noticed them… and the first, I still might not have caught had it not been pointed out to me.

The first one is subtle. Right before making your choice, at the end of the pathway, right as the ending goes into full cut-scene mode (AAAARGH) the music changes. And right after the change, but before the soulful piano piece that now fills so many of us with rage and sadness… There is a brief musical cue. An interlude, if you will, separate from either track.

For Control and Synthesis, this cue is identical. It includes the distinctive sound of a reaper, and is dissonant and off-putting.

For Destroy, it is almost… Hopeful. Undeniably positive.

Listen for yourself at that point in all three paths and tell me I’m wrong. It’s there, and it’s deliberate, and it’s very obvious once you’ve heard it.

Music is never accidental in a big budget game, nor in a film. If that sound is there (and it is), it is there for a purpose. It is there for you, the player, to hear… even if you’re not consciously aware of it. It had to be written, uniquely for that moment. Especially for a cut-scene or a transition like that one.

The next point is a more common one. In the Control and Synthesis endings, Shepard’s eyes take on the appearance of Saren’s or The Illusive Man’s. The eyes of someone who’s been indoctrinated. And once again, we’re given a close-up to emphasize the detail. We see Shepard’s skin pulling back to reveal the same kind of metallic substance we saw on The Illusive Man’s face minutes ago. And then, we see Shepard seemingly die.

I remind you, close-ups tell the story. They highlight details the developers want you to notice.

In destruction, those visual cues do not appear. We see Shepard’s eyes are his own. We get a close-up, again, to hammer this point home. We see Shepard idiotically walking toward the exploding tube in a very purposeful manner, and then…


For once, Illusive Man, we DO agree.

We get the same bullshit “visions of hope” in all three choices, assuming your EMS was high enough to not destroy the universe by mistake. And if your EMS is high enough, in the destroy ending… You get that ridiculous teaser of Shepard breathing in rubble that does NOT look like anything on the citadel. At all. Especially if (as some of the writers have evidently asserted) the citadel isn’t destroyed in any of the endings.

And several have pointed out that it’s possible to see EDI alive in the Red ending if she was in your final squad…

Shepard breathes that last breath only in the destroy ending… despite the child’s claims that it would kill you, as well, on the grounds that “even you are part synthetic.”

Legion's sacrifice might not have been in vain.

Explanation? Simple. The kid is lying. I mean, seriously. He’s trying to con us. Make the two endings he favors (Control, Synthesis) appear as “good” as possible by claiming that the consequences of the red ending will be dire. The Geth are incredibly sympathetic characters, and the little brat knows it. He lies to you to make you hesitate to do what you have ALWAYS known you had to do. It’s a hostage situation, and he thinks he can use the Geth as shields to protect the reapers from your wrath.

Simple fact: we have no more reason to accept his word on the consequences of our choice than we do to accept that his “solution” is better than ours, and everything about this scene is designed to make us question his statements. We, the players, have to take the step he tries to steer us away from… and yes, that includes illogically shooting the exploding glass tube.

So why won’t BioWare just admit that this is what they meant?

When asked about Indoctrination Theory, the panel at PAX refused to confirm or deny it. Jessica Merizan has also refused to refute it on the grounds of “liking literary analysis,” which honestly is probably true (and let’s not forget, she is a fan, like us, and may not have the information she’d need to officially confirm or deny it anyway. And as always, the disclaimer that her tweets represent her own opinion and should not be taken as “word of God/Dev” applies. Be nice to her. She’s cool. Seriously. Don’t make me send out the owlbears, because I will.)

But I think there may be another reason why they haven’t confirmed it – despite the plentiful and now apparent clues that it MUST be true, or something like it. Keeping in mind that this is only speculation on my part (I know, we hate that word…)


I’m glad you asked. The answer is actually pretty simple.

Because they can’t.


They literally cannot tell us that this is true without completely destroying the point.

Think about it. If the entire point was for us, the players, to come to this conclusion on our own and wrestle with the damn thing, telling us it’s true ruins the puzzle. And if the theory is true, that would go against the entire purpose of the exercise.

Of course, the problem with this defense is that even if it’s NOT true, they probably still wouldn’t tell us, because it’s too brilliant. But let’s assume, for the moment, that we’re dealing with skilled writers here, and that they actually have crafted something incredible, if VERY frustrating.

My chief frustration in all this is that I was told before buying the game that it would be the end of Shepard’s story, and that this is not an ending: it is merely the place the writers stopped writing. If all this is meant to indicate that the real ending to the story hasn’t happened yet, I want to see what happens NEXT.

But now… I’m getting the distinct impression that BioWare has changed their tune.

Repeatedly since the outcry began, we have glossed over the message of the StarGazer (mainly because we were so ANNOYED by him after that perceived clusterfish* of an ending and the call to purchase more DLC while we were still emotionally fragile. It takes a real quad to ask someone for money after you’ve just kicked them in theirs.)

*Thanks to htewing for coining that one.

That message: One more story.

Blog posts from BioWare in response to our outcry have even casually (between all the apparent PR approved doubletalk and perceived marginalization of our collective voices) suggested the possibility of both story DLC and full Mass Effect games to come, along with the quote, you haven’t seen the last of Commander Shepard.

What do we do now?

We wait. There is every possibility that the free ending DLC (The Extended Cut) will clear this issue up, or at least make the game more satisfying without having to constantly play detective. Not that I’m against playing detective, mind you, but it is getting to be a bit of a headache.

We wait. We hold the line. We keep holding out for what we really need (the REAL end to the story and the fate of our friends) and support BioWare’s staff as best we can.

For me, there can only be one option.

I am an Indoctrination Theorist: I have Seen The Ending Within The Ending, and I Want to See What Happens When Shepard Wakes Up. I have Faith in BioWare, in Commander Shepard, and in my Fellow Gamers. I Trust that BioWare will Resolve This Controversy Well and Effectively, and Address Our Concerns, and promise that When they do so I shall Sing their Praises (and probably purchase everything I can find with a Mass Effect Logo On It). Until I Am Vindicated, I Will Hold The Line.

In loving memory of Marauder Shields, the first of us to fall.


15 responses to “Indoctrination Theory Confirmed: Or, How I learned to Relax and Love the BioWare

  • Breanna

    Great post. I’d be interested to hear what you think of my own blog on the subject. I took a much more negative attitude toward it, though that may have been because I wrote it before the “Extended Cut” was announced. Take a look, if you are so inclined:

    • Jonathan

      Clicked through – I’ll read it over and leave a comment when I’ve formed a response. Thanks!

    • Tahj

      I’ve actually written a series of blog posts in favor of the Indoctrination theory but against the Dream theory and would be interested in your comments. I’ve done some extensive research using the Mass Effect Wiki and have proved that Shepard has been indoctrinated with that info. I also work toward debunking the “Dream theory” as presented by Acavyos on Youtube. Check out the last of my four post series here at

  • AOPrinciple

    I agree 100% with you. Of course, neither of us can be 100% sure, but if you round up from 99.9%, well… The clues are there; the ending is so chock full of them, it’s far more a “theory” (in the diminutive sense) that the ending actually takes place in the real world. Here’s to keeping faith and trusting the developers, even if the process is maddeningly frustrating. Kudos.

    • Jonathan

      It certainly seems harder to support the idea that the ending takes place in the real world, given the many obvious logical inconsistencies introduced by that assumption…

      Not the least of which would be my earlier complaint about the “least intuitive user interface OF ALL TIME.” 🙂

      Glad you enjoyed the read.

  • Marti

    Great work, although I’m getting frustrated with all IT theorists claiming that we MUST choose destroy to get the real ending. Perhaps that wasn’t your intent but everyone seems to imply that waking up after destroy is the only way to wake up. As much as there are clues to the IT theory, there are as many clues to the game hammering into your skull that you can come back from indoctrination, at least definitely words that claim to interrupt the process. Remember there’s a whole campaign on sanctuary showing how Cerberus pulled it off. I mean they threw a lot of work into an entire plot just to say 1 thing, that TIM wants control. Something we already knew. It’s entirely possible that if you choose a path that indoctrinated you that ME4 starts off with your friends taking that Cerberus tech to save you. It wouldn’t vary too much from ending to ending. Even if you woke up, your friends will still have to find your tattered body while fending off harbinger. I personally kept my synthesis save because the idea of suddenly, desperately doing everything you can to save your shepherd is the most climactic for me, especially if he’s now become the enemy. It brings the entire story around, forcing the point that shepherd wasn’t strong because of himself, he got Subdued, even killed off in me2. His strength came from his friendships he forged, the loves he created, and the loyalty he earned. Every aspect of each relationship comes into play here rewarding you for each minute you spent getting to know your friends. That is the stark difference between shepherd and TIM, and Saren. That’s why being indoctrinated might actually be the more dramatic fulfilling choice. Plus… Given the amount of time you need to get synthesis ending makes me feel there’s also a little something extra on the other side, compared to basic control ending.

    • Jonathan

      Interesting perspective. I can see how that could make for a compelling story… I’m not sure how it would work on the surface, but maybe something could be done. I have a difficult time picturing a story like that of the reapers still existed, though…

      As I probably SHOULD have been clear on, this is just me reading the evidence as I see it, and presenting my findings.

      I would also point out that the amount of time needed to get the Synthesis ending is aproximately the same as the amount needed to get the “Shepard breathes” scene on Destroy. I’d have to double check the EMS requirements to be certain, but the two outcomes are reasonable close numerically. 🙂

  • Marti

    I could reason then there would be goodies for both outcomes since the amount of time pit into both would each warrant a cookie. So maybe “shepherd breathes” is the best possible renegade ending and synthesis is the best possible paragon option. These are just my own hopeful interpretations as well. I just hate being pigeonholed into 3 endings only to see that most interpretations of IT end up pigeonholing us into 1.

    • Jonathan

      I’d say in an ideally constructed ending the variation would come less from the choice made in that moment and more from all the important choices we’d already made over the game — something that needs to be corrected either way, because right now we don’t see that. We see one of 6 basically identical cinematics with no real variation, and that’s stupid no matter how we look at it. -_-

      And obviously, based on my entry above, I’d argue that destruction is not a renegade action here, since Paragon Shepard always argued for it, and Anderson can’t be wrong. 😉

  • AOPrinciple

    I have a question for you. I tried to look for some videos on teh ending that have clear enough sound to hear the audio cues you were talking about the correspond with the different paths. I can’t really tell what sounds or music you’re referring to. Is there a particular video you can suggest or a breakdown of the scene that highlights these points? Thanks agian.

    • Jonathan

      There are actually two, I’m told. I’ve only confirmed one of them for myself.

      There’s supposed to be one right in the middle of the walkway, where the paths branch. If you stand there, I am told, and then start walking toward one of the choices, you’ll hear the music shift briefly. It’s the same sound I describe in the article above. This, I haven’t personally confirmed yet, because I’d need either a video of someone DOING that, or to go into the game and do it myself. It’s on my to-do list.

      The second one is easier to hear, and any YouTube video of the whole path to an ending will let you pick it out. Listen RIGHT at the point where Shepard commits to the decision – shooting the tube, grabbing the rods, jumping into the green beam. There’s a distinctive sound again there, like the one I described – immediately before the “soulful piano music,” right as you lose control of Shepard for the final cinematic. The audio cues for Control and Synthesis are identical. The one for Destroy is different.

      As far as I know, there isn’t a video that actually highlights that sound, but it should be easy enough to pick out once you know where to look… And once you’ve heard it, it’s hard to miss. Hope that helps!

  • Destructor

    Great summary! I, too, am an Indoctrination Theory believer. If it is true, it will be one of the biggest mindf*cks in gaming… ever.

  • dean

    the thing that got me to even start looking at other theories than what’s presented in the game is the major continuity error of sheppard breathing in space!? throughout the games when Sheps been outside with unfavourable conditions, the helmet has been forced on. from the moment he walks out the tunnel, there is no reason that there should be any breathable air in his viscinity! ( the extended cut 4th ending was quite good just for how it caught me offgaurd, I shot the ai out of frustration on every playthrough ive done 😛 )

  • Scott

    The ending is sheer brilliance and, like your post says, Bioware can never comment on it without demolishing its genius. They didn’t only figure out a way to indoctrinate SHEPARD. They figured out how to indoctrinate THE PLAYERS THEMSELVES!

    For 2.99 games your singular goal has been “DESTROY REAPERS”. Nothing else mattered and you’d give anything, do anything, sacrafice anyone, to do it. Heading into the Priority: Earth mission, 100% of players were ready to blow the Reapers to kingdom come. 100%.


    The galaxy’s salvation – what you’ve been fighting for is RIGHT THERE WAITING FOR YOU TO TAKE IT. No more enemies. No more Geth Primes or Atlas’s or Banshees or Brutes…just a short, slow walk and one pistol shot and Shepard achieves his objective. The Crucible fires, the Reapers are destroyed and Shepard lives. You’ve won.

    But…two other options are put in front of you by THE BEING WHO TELLS YOU HE’S THE ONE CONTROLLING THE REAPERS. He’s THE enemy. THE bad guy. And he starts talking. And as he talks, he plays the guilt card.

    He tells you that you your new friends the Geth will die. Your squadmate EDI will die. He plays the fear card telling you that you are partly synthetic and YOU will die. He makes the option to let the Cruicble fire and Destroy the Reapers look like a crap sandwich.

    Then he sells you on two other options, one more extreme (Control), one middle ground (Synthesis) knowing full well – because he’s an ancient, super advanced machine – that when presented with three choices, most people will take the middle road.

    You sacraficed friends, lovers, entire star systems full of intelligent life (Arrival), War Assets who’ve died by the millions to get you to that point. All of them sacraficed their lives so YOU could take Shepard on the path where he could kill the Reapers.

    And then, the Reaper plays the guilt card on you, THE PLAYER. He could’t kill you with guns, explosives, biotics, or lasers. But he makes YOU, the PLAYER feel guilty for choosing an absolute. For choosing the victory you’ve fought so hard to get. He does it so masterfully in fact, that many PLAYERS chose the path that allows the Reapers to live.

    You, the player, are in control of Shepard. If you put down your controller and step away from your keyboard, Shepard stands idle until you return. Yet, in your moment of triumph, you have chosen to set aside your victory and side with the Saren (Synthesis), the Illusive Man (Control), and the Reapers.

    YOU, the PLAYER, have been indoctrinated into believing the Reapers. And that’s how the Reapers win.

    Brilliant. Just brilliant.

  • csm

    When asked about this theory at PAX 2012, Mike Gamble replied “we want the content to speak for itself”. When something speaks for itself (this theory), it doesn’t need explaining or confirming because it was meant to be pretty obvious.

    “confirmation that some fact or statement is true through the use of documentary evidence”

    Well judging by all the hints and clues in the ending, as well as the fact that Shepard is suffering every single symptom of indoctrination (according to the Indoctrination codex entry), that should be confirmation enough. Bioware was never going to come out and say “yeah, it’s true, that’s the ending”.

    That also leaves the fact that the Reapers are still there and they haven’t been defeated yet. As much as it hurts me to say this, Bioware stated before the game was launched that Mass Effect 3 is the end of *Shepard’s* story, not the Reapers. Either, Shepard gets indoctrinated along with everyone else, or he doesn’t.

    All that talk about choices not mattering in the last 5 minutes. Put it this way. Pick the control or synthesis option, and it essentially wipes out all your hard work. All those allies you recruited, all those choices you made are rendered moot, because every living thing in the galaxy is now indoctrinated. On the other hand, pick the destroy option (the supposed “bad” option), and you keep all that intact. No, they don’t show a cutscene of every choice, but the fact that the brat lies to you and at the end you wake up, when he said you and your friends would die, is pretty much a hint that he’s a big fat liar.

    Although some might think that the ending pigeonholes you into one ending, it was meant as sort of an indoctrination test. Pick the wrong answer, bad stuff happens. Pick the right answer, Shepard and everyone else lives.

    I am one who believes the entire game is the ending, not the last 5 minutes, which can play out differently. I did see my previous choices pay off along the way (in many ways in different playthroughs), so I’m not really bothered with only having one choice at the end.

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