Latest update: March 2017 - 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.

I have begun working on our massive rewrite of analysis for the Extended Cut endings and DLC. Hopefully I will get around to finishing this at some point in 2015, but it is a lot of work. Be sure to check back every month of so. Although if this is your first visit, there is a LOT to read already. Please let me know if you think I have overlooked anything or made any mistakes.


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

The Adventures of Commander Shepard GAME

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

The Mass Effect Andromeda trial came out via Origin Access' "Play First" scheme last night, offering 10 hours of play in the lead up to its full launch on the 21st. And my love for Mass Effect is so strong that I have sidelined playing The Legend of Zelda: Breath of the Wild for now (I'll still get some playtime in here and there thanks to the Switch's potable nature).

So far I have been able to play about 4 hours of the game and my excitement and desire to talk about this game demands I write up my thoughts so far. These will be SPOILER FREE single player impressions (have not touched multiplayer yet), so unless you are uber sensitive to even vague descriptions of scenarios then you should be fine...


Happy N7 day 2016!

We have some MASSIVE EXCLUSIVE NEWS coming some time next hopefully month! Was hoping to have it ready for N7 day, but it would have probably have been buried in the Andromeda trailer news. However stay tuned!!!

In the meantime, enjoy the Mass Effect Andromeda trailer -

It has been clear for some time that Andromeda avoids addressing the ending of ME3, but the new trailer lays that out as clear as ever. Hundreds of years after the events of Mass Effect 3 and taking place in the Andromeda galaxy, you are the "Pathfinder".

Also backwards compatibility was announced for the original trilogy on Xbox One, and all games are available through EA Access!

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.

Well maybe 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 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 give 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 its 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.

Hopefully I will have time to write part 2 soon. But until then, I recommend continuing reading my pre-EC analysis, which is still very relevant and continues from the logic above nicely.

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