Latest update: February 2021 - See Updates

Welcome to Mass Effect Indoctrination, a site dedicated to detailed analysis of the Mass Effect series with the Indoctrination Theory interpretation of the endings of Mass Effect 3 the main focus.

Since the launch of this site in April 2012 it has become widely considered one of the main sources for analysis of the Mass Effect 3 ending and for the Indoctrination Theory.

For many people the endings of Mass Effect 3 when taken at face value are unsatisfying at best and thematically offensive at worst. However many Mass Effect fans believe that Bioware intended there to be multiple interpretations of the endings that go beyond a simple literal reading. In fact Bioware have said as much.

Some people will say these interpretation are all "head canon", or that we are merely grasping at emergency induction ports in order to make ourselves feel better about how the series ended. Well maybe that's true. But I do know that all this analysis and speculation about the endings of Mass Effect 3 has actually greatly contributed to my and many other fans love of the series rather than detracted from it. And I know the way I view the endings gives me great pleasure. And I would much rather interpret the fiction in a way that makes it better than in a way that almost destroys it.

Over the coming months expect some new content as we examine the new Legendary Edition remaster of the trilogy!


All worthy work is open to interpretations the author did not intend. Art isn't your pet — it's your kid. It grows up and talks back to you.

- Joss Whedon

Legendary Edition has landed!


It's finally here! I have been away working until today but look forward to some new deep dives over the coming months as I work my way through the trilogy again :)

SIDE EFFECT: The Adventures of Commander Shepard GAME

UPDATE: May 17th 2021

To celebrate the Mass Effect Trilogy remaster we are working on a "Legendary Edition" demake! This new version will "remaster" the graphics in an older pixel style to more accurately reflect classic LucasArts games and will include some if not all of the following features (and more) -

+ Full voice acting!
+ New puzzles and dialog!
+ More Paragon and Renegade choices!
+ The ability to play as Fem-Shep or M-Shep!
+ All new art and animations!
+ Translations into other languages! (hopefully Russian and German at least)
+ And more!

Coming in 2021!


Surprise! So my secret Mass Effect project is finally ready. Now you all know why my long delayed rewrite of Mass Effect Indoctrination fell to the wayside. For the last year I have been working on a Mass Effect fangame. A point and click "demake", The Adventures of Commander Shepard is a satire of Mass Effect and a love letter. You also find a healthy amount of references to the Indoctrination Theory. Here is the blurb from our new site:
 While Mass Effect Andromeda won't see his return, Commander Shepard, still has one more
adventure in him!

A fan project and driven by a passion for classic point and click adventure games and more importantly the Mass Effect series; The Adventures of Commander Shepard is a fan-fiction “demake” and love letter to both.

Driven by our intense love for Mass Effect and our inability to let it go after Mass Effect 3, this project first began as a animated satire but soon grew into a full point and click adventure game. There is so much about Mass Effect that lends itself perfectly to the classic point and click genre, and we felt that trying to bring in some of the old LucasArts humour while poking fun at some of the tropes of the modern RPG was something that really helped blend the two together in a fun way that made our little fan-fiction “demake” the perfect homage to both. We hope you enjoy playing through this passion project as much as we enjoyed creating it.

 Download here

Part 1 - Let's start at the end...

There is something wrong with the end of Mass Effect 3. No it is not that it is bad. In fact I think it is utterly brilliant in many ways. I think most peoples issue with the end is the very existence of the Control and Synthesis choices. I know that if taken literally and at face value, I find those endings absurd and insulting to the narrative of the series thus far. Those choices are illogical at best and thematically at odds with the rest of the 3 games.

Taken from lead writer Mac Walters' page of notes on the ending.
Some argue that Bioware just wrote a bad ending. Some argue that there is something deeper going on and that Bioware wrote a twist into the ending. A twist designed to elicit speculation. A twist they have no intention of revealing (or at least not any time soon). Some go as far as to say that twist is that everything after Harbingers beam hitting Shepard is an indoctrination induced hallucination. Others believe just what we see after we make our final choice is an hallucination.

Well maybe some of it is, and maybe it isn't. But as far fetched as it may seem on the surface, there are good arguments to support this theory. And I will examine them in due time. There are also other ways to view the endings, and I will get to those too. But most import of all, you do not have to believe in any form of the so called "Indoctrination Theory" to follow me on this breakdown and examination of the issues with the endings of Mass Effect 3. I would argue that the more we discuss and analyze the ending, the more enjoyment we will get from it. And even if the writers come out and spell out exactly how they intended to interpret the endings, and we don't like it... well we can still discuss why and how it can be interpreted to be better.

But long before we get to any of that, there is a very important argument to be made that almost all other arguments hinge upon. One that once accepted turns the entire ending of Mass Effect 3 on its head...

Note: This analysis will be including discussion of the Indoctrination Theory. If you are new to the Indoctrination Theory it is a very good idea that you first start here before proceeding.

Section 1: You can not trust the Catalyst!

In my opinion this is where all speculation on the endings begin. Once we establish that we have every reason to be extremely sceptical that anything the Catalyst tells us is true, then a whole plethora of analysis is required to establish what we should believe.

Since the release of the EC and even more importantly the Leviathan DLC, our understanding of what the Catalyst is has come a very long way. Thankfully it is now more than a literal Deus Ex Machina to resolve the games plot.

Some argue that the Leviathan DLC did nothing more than try and foreshadow and justify the arguments of the Catalyst. I would argue there are a few very good reasons to suggest it does the opposite and undermines the Catalyst, its motives and its methods.

What does appear to be true though is that an ancient race known to us as the Leviathans created an AI known merely as "The Intelligence" in order to solve a problem. And it would appear that the Catalyst and "The Intelligence" are one and the same.

The first major issue with trusting the Catalyst is trying to understand what the problem it was created to solve is supposed to be. The issue is that the Leviathan and the Catalyst describe what this problem is very differently.

The Leviathan's version of events -
Before the cycles, our kind was the apex of life in the galaxy. The lesser species were in our thrall, serving our needs. We grew more powerful, and they were cared for. But we could not protect them from themselves. Over time, the species built machines that then destroyed them. Tribute does not flow from a dead race. To solve this problem, we created an intelligence with the mandate to preserve life at any cost. As the Intelligence evolved, it studied the development of civilizations. Its understanding grew until it found a solution. In that instant it betrayed us. It chose our kind as the first harvest. From our essence, the first reaper was created. You call it Harbinger. 
The Intelligence has one purpose: preservation of life. That purpose has not been fulfilled. It directed the reapers to create the mass relays - to speed the time between cycles for greatest efficiency. The galaxy itself became an experiment. Evolution its tool.

And this is how the Catalyst explains it -
I was created to bring balance. To be the Catalyst for peace between organics and synthetics. 
By ones who recognized that conflict would always arise between synthetics and organics. I was first created to oversee the relations between synthetic and organic life. To establish a connection. But our efforts always ended in conflict. So a new solution was required . 
When they asked that I solved the problem of conflict, they failed to understand that they were part of the problem themselves. The flaws of their organic reasoning could not perceive this. They lacked the foresight to understand their destruction was part of the very solution they required. 
They created me to oversee the relations between synthetics and organic life... to establish a connection. They became the first true reaper. They did not approve, but it was the only solution.

We have a pretty huge discrepancy here. Leviathan states the Intelligence was created with a mandate "to preserve life at all cost". But the Catalyst claims it was created to "bring balance. To be the Catalyst for peace between organics and synthetics" and to "oversee the relations between synthetic and organic life". These are very different things.

From the Leviathans point of view the entire reason The Intelligence was created was to protect advanced organic races from being destroyed by the synthetics they created. Because those organic races were essentially slaves to the Leviathan's. Paying them "tribute", and as they say "Tribute does not flow from a dead race".

Leviathan never mentions wanting The Intelligence to forge peace between organics and synthetics, they do not appear interested in "peace" or "balance". The mandate is clear...


So what does the Catalyst decide to do? Not only wipe out all advanced organic races and "preserve" them as goo in giant synthetic machines used to wipe out all advanced organic life in the next cycle. But do the same thing with its creators! The "preserved" organics can no longer "pay tribute" effectively in their new goo like form. But worse than that there is also no race left to pay tribute too!

This is only preservation in the way we preserve strawberries in jam. It certainly does not appear to be in any way what the Leviathans intended.

Maybe the Leviathans were not clear enough and the AI just had a radical interpretation of how to fulfill its task? Seems unlikely they would create an advanced AI and then not be clear as to its purpose. Especially as from the account given it sounds like it took some time to come to its conclusion, evolving as it studied the development of civilizations.

And then worst of all, when it decided to slaughter its creators and turn them into Reaper jam, it didn't even bother to explain to them why!

There can be no doubt that the Leviathan's could not trust the Catalyst. So why should we?

I would argue that this discrepancy shows that the Catalyst is no longer attempting to fulfill its original task but has decided itself to achieve something outside its original parameters. Namely that it has decided to create its own apex of evolution, The Reapers.

It pays "tribute" to its creators by building its creation in the image of the Leviathans. Why did it do this? Maybe it decided its creators mandate had a fundamental problem. Maybe it had a radically different interpretation of what "life" was. Maybe it decided that Synthetics were also "life" and therefore to preserve life it had to eliminate anything that risked the continued existence of Synthetics, namely the Leviathans who were unable to control Synthetics in the same "thrall" they could control organics and wanted them out of the way.

Maybe the Catalyst's twisted perception of what "life" is leaves it fully satisfied with Reaper goo being a preservation of life. Being that it turns organics into a form of life closer to Synthetic life, which it finds easier to understand as it is synthetic itself. And if it decided that the way to solve any conflict was to be able to control both organics and synthetics, it does this successfully with a more advanced version of the "thrall" know to us as "indoctrination".

I think what we have here is a perfect example of an AI going off the reservation, of a creation rebelling against its creator.

Which brings us the the next problem with the Catalyst's version of events.

What Synthetic rebellion?

The Catalyst justifies the need for the "harvest" by stating that "The created will always rebel against their creators" and that "Without us to stop it, synthetics would destroy all organics".

But there is simply no evidence for this OTHER than the Catalyst itself!

Sure the Leviathan backs this argument up to a small degree, saying that "Over time, the species built machines that then destroyed them.".

But even that claim does not at all suggest that the synthetics then wanted to eradicate all organic life.

And worse of all, across the span of three games Shepard's experience has been that synthetics are not at all hostile towards organics. The Geth merely defended themselves from a preemptive attack from the Quarians. The Quarians that were the aggressors and as soon as the Quarians gave up their attempts to wipe out the Geth, the Geth immediately forgive them and help them reestablish life on their home planet.

So not only do the Geth not rebel against their creators but given the chance, they immediately forgave their creators and preferred peace and cooperation. Their instant act of forgiveness not only showing the possibility of peace between organics and synthetics without the Catalysts involvement, but also suggesting that the Geth were very unlikely to desire the eradication of all organic life.

Not to mention Shepard's friendship with Legion and mutual trust between them.

Then we have EDI, an unshackled AI that strives to become more human. Who freely sides with organics and is integral to the struggle against the Reapers. Not only does she display no evidence of ever wanting to rebel against her creators, but she essentially falls in love with an organic (Joker). EDI even states that she would be willing to die for Joker.

The only evidence of hostility from synthetics against organics is the Reapers themselves and when they indoctrinate Synthetics into aiding them. Which we see with the Geth that aid Saren and the heretics.

Javik backs this up with this description of the most advanced synthetics of his time -
In my cycle, a race called the Zha used machines, the Zha'til, as synthetic symbiotes. The Reapers subjugated the Zha'til as they have the geth. Their mechanical swarms blotted out the sky. They were brutal, merciless.
He never gives any example of any other synthetic race rebelling against their creators.

The only synthetic life that desires wiping out organic life we have experienced has been the Reapers which are controlled by the Catalyst. There is simply no evidence in any of the games to suggest that it is inevitable that synthetics will one day wipe out all organic life.

So if we are to conclude that the Catalyst is telling the truth, then we have to conclude that Bioware have made some terrible thematic choices and story telling failures in this regards.

However it makes more sense to conclude that the Catalyst is either mistaken, or lying in order to manipulate Shepard's choice.

Which brings us to...

The Leviathan meeting proves that the Catalyst meeting is at least partly an hallucination!

Upon meeting Leviathan Shepard is aboard a Triton mech and in the depths of the ocean planet 2181. There can be no doubt that this encounter is mostly an hallucination.

Shepard goes from experiencing this encounter from inside the Triton, facing the massive Leviathan itself. To a full on hallucination in which the Leviathan takes the form of people from Shepard's memory.

The Leviathan pretty much spells out that what it is doing is a form of indoctrination, or the "thrall" as it calls it.

Your mind belongs to me. Breathe.

Your memories give voice to our words. Your nature will be revealed to us. Accept this.

When fully pulled into this hallucination, Shepard is on all fours and approached by the Leviathan in the form of Doctor Ann Bryson.

The similarity between this event and the moment Shepard comes face to face with the Catalyst can not be understated. This is no coincidence. Bioware intentionally made it very obvious that the meeting with the Leviathan was an hallucination. And they made sure the event was almost identical to the meeting with the Catalyst so we knew that at least parts of that meeting were also an hallucination.

And we know for certain that the Catalyst is in Shepard's mind in order to manifest in the image of the little boy that only Shepard knows about. And we can therefore conclude it chooses the image of the boy in order to illicit sympathy from Shepard. To make Shepard more open to what it has to say.

Knowing that Leviathan uses an almost identical method of hallucination/mind control in order to make Shepard its slave -
You will remain here as a servant of our needs.
And from concluding from the previous section that we cannot trust the Catalyst, then we can assume that it is attempting to manipulate Shepard to its way of thinking. Indoctrinating if you will, Shepard into doing what it wants.

We even have to question if anything Shepard experiences from this point is real. Since the encounter with Leviathan is all an hallucination, how do we know any element of the meeting with the Catalyst isn't one?

It is from this point that we have very serious cause to question the choices the Catalyst offers Shepard.

Which will bring us to Part 2, in which I will examine the choices the Catalyst lays before Shepard and question its motives for doing so.

From here on all the analysis was done prior to the Extended Cut, but I do not think the EC made much impact on any of this analysis. So it is presented without change. After the Legendary Edition is out I will write a whole new examination that takes into account anything new from the Legendary Edition and re-examines any changes the Extended Cut made.

READ the Pre-EC Analysis - Evidence for Indoctrination

Kotaku: Mass Effect 3‘s Ending Disrespects Its Most Invested Players

Take a look at this excellent critique of the pre-EC endings of Mass Effect 3 when taken at face value. Especially this section which further backs up why we should distrust the Catalyst's narrative.

However, I think they are wrong on their main point. I believe the ending actually rewards Mass Effects most invested players. For those of us invested enough to analyse the ending in detail, we are rewarded with not only the joy of this analysis but with an interpretation of the ending that is simply brilliant.

The larger problem for the ending, though, is that it leans on the series' least interesting theme, and even then disregards everything that the games have conveyed on the subject.
After all, the genuine synthetic intelligences present throughout the series have generally not been inimical to organic life. The robotic Geth, although initially presented as aggressive foes, are later shown to have been the victims of pre-emptive attacks by the Quarians. Even the ones that joined the Reapers in the first game did so out of a desire for self-advancement, not out of intrinsic malice towards organics. The other true AI the series presents is EDI, whose voluntary aid repeatedly proves crucial in helping Shepard's missions succeed, and who might even be in love with Joker. Though the game undercuts itself by almost always placing synthetic lifeforms on the business end of Shepard's gun, in dialogue and plot the synthetics are neutral, or even allies.
Yet even though the story of the Mass Effect games refutes the necessity of war between AI and organics at every turn, the finale presents their conflict as inevitable. The ending does not even give Shepard the option to use the truth about the Geth to argue against the Catalyst that controls the Reapers.


In support of the Reject ending

Take a look at this is a fantastic article in support of the reject ending from Forbes. I think his logic collapses in suggesting that Reject is superior to Destroy because Shepard cannot be sure the Catalyst is not lying. Because even if the Catalyst is lying, Shepard would still have all the benefits of the Reject ending while still having a shot at Destroy being a possibility.

Why hope that a future species can win this with the data Liara has left when you have a chance at winning this war right now without putting Liara's data beacon at risk? The only downside to Destroy is the loss of the Geth and EDI, and since Reject will still lead to losing them and everyone else I see no benefit.

However his argument on why Shepard should not trust the Catalyst is excellent and well worth a read.

Let’s stay inside the narrative for the moment. When Shepard reaches the Citadel, and meets the guiding intellect of the entire megillah, she is presented with up to three immediate options, depending on her success in rallying and readying forces:
  1. Destroy the Reapers, at the cost of the lives of the Geth, her crewmate EDI and herself.
  1. Control the Reapers
  1. Render the Reapers’ mission meaningless by combining organic and synthetic life, thus ending the cycle of synthetic/organic violence
None of these are perfect options – and, of course, Shepard is not aware that she is a video game character, and thus has no reason to believe that these options are actually true. To quote myself:
Think of it like this: if you were exploring a dungeon, and suddenly came across a blue potion of unknown provenance, would you drink it? Probably not. If your character does the same, you will think nothing of telling the character to drink it. Blue potions have thus far restored magical power, and this should be no exception. And, if it turns out to be poison, the penalty is relatively minor – having to restart the level, say.
BioWare has given Shepard another option – to refuse to drink the red, green or blue potions, in effect – and although it may not look like a happy ending, it is by no means an unrealistic or frame-breaking one.
So, the rejection ending. From Shepard’s point of view, none of those options are viable. Either she does not trust the mysterious new character offering them, or she will not sacrifice billions of Geth, even if the alternative is most likely the extinction over the coming decades or centuries of the Geth and many other races. Or she very wisely does not believe that she can control the Reapers, or that even the remarkably advanced science that created the Reapers could amend the DNA of every being in the universe.
She’s got a point.

FULL ARTICLE: The Real Hero Of Mass Effect Explains How - And Why - The 'Reject Ending' Works

Conversation with the Catalyst

For reference here is the full conversation with the Catalyst from the Extended Cut. This is with Paragon conversation choices and maximum EMS. Conversation choices are in grey.

Catalyst: Wake up..

Shepard: What? Where am I?

Catalyst: The citadel it’s my home.

Shepard: Who are you?

Catalyst: I am the Catalyst.

Shepard: I thought the Citadel was the Catalyst.

Catalyst: No. The Citadel is part of me.

Shepard: I need to stop the Reapers, do you know how I can do that?

Catalyst: Perhaps. I control the Reapers. They are my solution.

Shepard: The solution to what?

Catalyst: Chaos. The created will always rebel against their creators, but we found a way to stop that from happening. A way to restore order.

Shepard: By wiping out organic life?

Catalyst: No. We harvest advanced civilizations, leaving the younger ones alone. Just as we left your people alive the last time we were here.

Shepard: But you killed the rest?

Catalyst: We helped them ascend so they could make way for new life. Storing the old life in Reaper form.

Shepard: I think we’d rather keep our own form.

Catalyst: No you can’t. Without us to stop it, synthetics would destroy all organics. We’ve created the cycle so that never happens. That’s the solution.


Shepard: You said you’re the Catalyst but what are you?

Catalyst: A construct. An intelligence designed eons ago to solve a problem. I was created to bring balance. To be the Catalyst for peace between organics and synthetics.

Shepard: So you’re just an AI?

Catalyst: In as much as you are just an animal. I embody the collective intelligence of all Reapers.

Shepard: But you were created?

Catalyst: Correct.

Shepard: By who?

Catalyst: By ones who recognized that conflict would always arise between synthetics and organics. I was first created to oversee the relations between synthetic and organic life. To establish a connection. But our efforts always ended in conflict. So a new solution was required.

Shepard: The Reapers?

Catalyst: Precisely.


Shepard: Where did the Reapers come from? Did you create them?

Catalyst: My Creators gave them form. I gave them function. They in turn give me purpose. The Reapers are a synthetic representation of my creators.

Shepard: And what happened to your creators?

Catalyst: They became the first true Reaper. They did not approve, but it was the only solution.

Shepard: You said that before, but how did the Reapers solve anything?

Catalyst: Organics create synthetics to improve their own existence, but those improvements have limits. To exceed those limits, synthetics must be allowed to evolve. They must by definition surpass their creators. The result is conflict, destruction, chaos. It is inevitable. Reapers harvest all life. Organic and synthetic, preserving them before they are forever lost to this conflict.

How is “this” not conflict?

Shepard: We are at war with the Reapers right now.

Catalyst: You may be at conflict with the Reapers but they are not interested in war.

Shepard: I find that hard to believe.

Catalyst: When fire burns, is at war? Is it in conflict? Or is it simply doing what it was created to do? We are no different. We harvest your bodies, your knowledge, your creations. We preserve it, to be reborn in the form of a Reaper. Like a cleansing fire, we restore balance... New life both organic and synthetic can flourish.


Shepard: What do you know about the crucible?

Catalyst: The device you refer to as the crucible is little more than a powers source. However in combination with the citadel and the relays it is capable of releasing tremendous amounts of energy throughout the galaxy. It is crude but effective and adaptive in it’s design.

Shepard: Who designed it?

Catalyst: You would not know them and there is not enough time to explain. We first noted the concept for this device several cycles ago. With each passing cycle the design has no doubt evolved.

Shepard: Why didn't you stop it?

Catalyst: We believed the concept had been eradicated. Clearly organics are more resourceful than we realised.

We’re just trying to survive!

Shepard: But you’re taking away our future, without future we have no hope. Without hope we might as well be machines, programmed to do as we are told.

Catalyst: You have hope, more than you think. The fact that you are standing here, the first organic ever proves it. But it also proves my solution won’t work any more.

Shepard: So now what?

Catalyst: We find a new solution.

Shepard: Why are you telling me this? Why Help me?

Catalyst: You have altered the variables.

Shepard: What do you mean?

Shepard: The crucible changed me, created new... possibilities. But I can’t make them happen. If there is to be a new solution. You must act. It is now in your power to destroy us. But be warned, others will be destroyed as well. The crucible will not discriminate. All synthetics will be targeted. Even you are partly synthetic.

I want details.

Shepard: What exactly will happen?

Catalyst: Your crucible device appear to be largely intact. However the effects of the blast will not be constrained to the Reapers. Technology you rely on will be affected. But those who survive should have little difficulty in repairing the damage... There will still be loses but no more that what has already been lost.

It will end the war?

Shepard: But the Reapers will be destroyed?

Catalyst: Yes but the peace won’t last. Soon your children will create synthetics and then the chaos will come back.

Shepard: There has to be another way.

Catalyst: There is, you could instead use the energy of the crucible to seize control of the Reapers.

Shepard: So the Illusive man was right after all?

Catalyst: Yes but he could never have taken control, because we already controlled him.

Shepard: But I can?

Catalyst: You will die, you will control us but you will lose everything you have.

I don’t understand.

Shepard: How can I control the Reapers if I’m dead?

Catalyst: Your corporeal form will be dissolved. But your thoughts and even your memories will continue. You will no longer be organic. Your connection to your kind will be lost. Although you will remain aware of their existence.

I think I understand...

Shepard: But the Reapers will obey me?

Catalyst: Yes. We will be yours to control and direct as you see fit.

Shepard: Hmm...

Catalyst: There is another solution... Synthesis.

Shepard: And that is?

Catalyst: Add your energy to the crucibles. The chain reaction will combine all synthetic and organic life into a new framework. A new DNA.


Shepard: Explain how my energy can be added to the crucible.

Catalyst: Your organic energy. The essence of who and what you are, will be broken down and then dispersed.

Shepard: To do what exactly?

Catalyst: The energy of the crucible, released in this way will alter the matrix of all organic life in the galaxy. Organics seek perfection through technology, synthetics seek perfection through understanding. Organics will be perfected by integrating fully with synthetic technology. Synthetics in turn will finally have understanding of organics. It is the ideal solution. Now that we know it is possible, it is inevitable we will reach synthesis.

Shepard: Why couldn't you do it sooner?

Catalyst: We have tried... a similar solution in the past. But it has always failed.

Shepard: Why?

Catalyst: Because the organics were not ready, it is not something that can be... forced. You are ready and you may choose it.

That’s a big change.

Shepard: You’re asking me to change everything, everyone. I can’t make that decision. And I won’t.

Catalyst: Why not? Synthetics are already part of you. Can you imagine your life without them?

Shepard: That is beside the point.

Catalyst: Your time is at an end, you must decide.

Then let’s end it.

Shepard: Let’s get this over with.

Catalyst: Do what you must.