Monday, May 14, 2012


Thanks everyone for making this guide so popular. It has gown so large (around 150,000 words) that I felt it deserved to be moved to a dedicated site.

Please see the new site here -


Friday, April 13, 2012

INDOCTRINATION: The Definitive Guide to the Mass Effect 3 Ending Controversy?








2012-05-14: Added info on reused foliage asset from dream sequence. Added info on Shepard's gun changing when selecting Destroy. Added BecomeAReaper code. Added more info on 1M1. Added comparison image for Breath scene object.
2012-05-10: Updates on Plot ID's. More Dream Foliage evidence. Converted more video links to embedded video. Added ReaperIndoc files. Added video proving Control as only option after saving Collectors base. New tree reflection image.
2012-05-09: Added Dream Foliage! Added all 6 endings as embedded video.
2012-05-04: Added section about the tree reflections in the decision chamber. Started Twitter section.
2012-04-24: Added info on plot ID's. Added thoughts on the Prothean VI. Added note on TIM's Predator gun.
2012-04-23: Added more screenshots and analysis showing the dream dissolve in 2c. Added section 5 dealing with the problems with Indoctrination. Added link to Lit Professor's analysis.
2012-04-18: Corrected some information and errors.


Welcome to what I hope to be one of the definitive sources for information and analysis of the Mass Effect 3 ending and especially the "Indoctrination Theory". If you think this guide is missing any information or you see any incorrect information, please do not hesitate to let me know.

When I first played the ending of Mass Effect 3 I was convinced Bioware had pulled some amazing sneaky subtle trick on me, but I just wasn't sure what it was.

I knew as soon as I saw the Catalyst manifest as the child from Shepard's dreams that something was wrong, and after being told my choices I paused the game for 20 minutes to consider what that might be. Ultimately I decided that the Catalyst was lying to me and that his manifestation as someone only Sheppard knew about must have something to do with Indoctrination.

Based on this I chose Destroy.

When my final moment showed Sheppard alive and taking a breath I was convinced I had made the right choice. However make no mistake I was still utterly confused by the ending. I did not think it was all a dream from the beam onwards and I did believe the choice I made actually happened.

The next day I spent hours on the internet reading people's fantastic interpretations of the ending, and other very legitimate criticisms of those interpretations. I also read how many people were angry and unhappy with the ending when taking it literally.

When I found the so-called "Indoctrination Theory" I was utterly convinced it was Bioware's intent. The only other option seemed to be that after 100's of hours of brilliant writing and a history of great storytelling Bioware managed to screw up the ending so bad that it made very little sense.

That said there has been significant moments where arguments against IT have seemed very persuasive to me. And I certainly believe it is possible that the Indoctrination Theory is wrong, and at the very least probably only partially explains Bioware's intent; but I am also convinced the literal interpretation could not possibly be 100% true either.

Many fans have done an incredible job of putting foreword arguments and evidence on both sides of the debate. And others have asked for someone to compile as much of it as possible into a single location.

Having spent many many hours over the weeks since completing the game reading these argument, I have taken it upon myself to be that person. And while I still strongly lean towards the Indoctrination Theory I very much intend to show both sides as objectively as possible.

The evidence should speak for itself and I will try not to let my beliefs effect how I present the evidence.

After all like any theory, the only way to "prove" it is to fail to disprove it. Any good scientist works very hard to try and disprove a theory they believe to be true.

I will also not be presenting the so-called "Indoctrination Theory" as some complete theory that has to be taken as a whole. Because I simply do not believe that is the case. It is quite likely in my opinion that some parts of the so-called theory contain truth while others do not. So it should not be argued as a complete theory wherein if any part is proven false the rest should be discarded. Just as we should not discard the literal interpretation simply because we can prove that any element of it is inaccurate.

0. Background information

Let's make sure we are all on the same page here.




0a. The Indoctrination Theory

For anyone reading this that has yet to be exposed to any form of the "Indoctrination Theory", I think we should establish some important elements first. First of all I strongly recommend this video.

It's not the definitive interpretation but it is an excellent summation of the basic idea and one of the most import early sources for convincing people there is something to the theory.

Also if you are interested in seeing an extensive analysis like this guide but in video format. Allow me to recommend this - The Indoctrination Theory - A Documentary

0b. What is Indoctrination?

Let's consult the Codex -

Reaper "indoctrination" is an insidious means of corrupting organic minds, "reprogramming" the brain through physical and psychological conditioning using electromagnetic fields, infrasonic and ultrasonic noise, and other subliminal methods. The Reaper's resulting control over the limbic system leaves the victim highly susceptible to its suggestions.
Organics undergoing indoctrination may complain of headaches and buzzing or ringing in their ears. As time passes, they have feelings of "being watched" and hallucinations of "ghostly" presences. Ultimately, the Reaper gains the ability to use the victim's body to amplify its signals, manifesting as "alien" voices in the mind.
Indoctrination can create perfect deep cover agents. A Reaper's "suggestions" can manipulate victims into betraying friends, trusting enemies, or viewing the Reaper itself with superstitious awe. Should a Reaper subvert a well-placed political or military leader, the resulting chaos can bring down nations.
Long-term physical effects of the manipulation are unsustainable. Higher mental functioning decays, ultimately leaving the victim a gibbering animal. Rapid indoctrination is possible, but causes this decay in days or weeks. Slow, patient indoctrination allows the thrall to last for months or years.

1. The Evidence for Indoctrination

I would like to begin with the strongest evidence to support the idea that Shepard is being influenced by Indoctrination and move on to lesser convincing evidence that is still worthy of consideration.

If anyone believes there is any important information or ideas/theories I have missed please let me know and I will be sure to add them.

The Strongest In-game Evidence for Indoctrination

1a. The Boy as the Catalyst

Bioware put a lot of effort into making the presence of this boy in the game important. Shepard watching him through a window is one the opening scenes of the game. Then after his death during the Reaper invasion Shepard has very strange recurring dreams of this child (see 2c).

These dreams include "ghostly presences" made of "oily shadows" and voices can be heard whispering that at times sound rather alien. The codex mentions hallucinations of ghostly presences and alien voices as an effect of Indoctrination, the Rachni Queen mentions "oily shadows" as an effect.

All rather tenuous of course, however when reaching the Catalyst Shepard meets a ghostly VI-like being that claims to be the Catalyst and manifests as the boy from these dreams. A boy Shepard has never mentioned to anyone and should have no significance other than Shepard's guilt at not being able to save everyone.

I would argue that we can conclude one of a few possibilities from this:
  • The Catalyst has access to Shepard's mind and chooses something familiar to Shepard to manifest as. In which case why does it choose to manifest as the boy Shepard feels guilt over? Is it to manipulate Shepard's choice? And is there any precedent for Reapers being able to read minds?
  • That the meeting of the Catalyst is actually taking place in Shepards mind just like the dreams.
  • Or the Catalyst is one of those hallucinations of ghostly presences the Codex mentions in regards to Indoctrination.
It would seem that any of these conclusions at least give weight to the idea that Indoctrination is playing a role in this final event.

The Best Counter-Argument

We do not know the extent of the Catalysts abilities after all he does claim he controls the Reapers. He may simply be able to read minds and chooses to manifest as an image of someone the person feels sympathetic to. The fact this is not explained could just be poor writing.

1b. The Dream Like Quality's of the Decision Chamber

While there are a great many things that are strange between Shepard being hit by Harbingers laser and arrival at the Catalyst, it is the "decision chamber" itself that stands out as the most unusual to me.

As soon as Shepard passes out trying to reach the control panel when Admiral Hackett calls to say nothing is happening (even though the arms are not fully extended yet), Shepard is bathed in a white light and a platform floats up to the decision chamber. Which just so happens to be in the place where Shepard collapsed.

If you have a high EMS the Catalyst's first words to you are "Wake up", even though Shepard does not actually appear to be unconscious at that moment, just crouched on all fours in pain. If your EMS is low he says "Why are you here?".

Everything the Catalyst says is echoed at the same time with the voice of both female Shepard and Male Shepard, coming from the left and right speaker respectively. A clue that the Catalysts voice is in Shepard's mind?

Even Shepard's words are echoed with whispers of Shepard's own voice. It all sounds very strange and unreal and gives the entire event a feeling of unreality.

And for some reason Shepard for the first time ever does not question any of the information imparted. Shepard has no questions or doubts about anything the Catalyst says?

Add this all to the fact that the Catalyst appears as the child in Shepard's dreams and you are hard pressed not to conclude something is simply not right here. Effects of Indoctrination certainly seem plausible.

The Best Counter-Argument

At this point Shepard is severely injured. This could easily contribute to experiencing things in a weird way, Shepard is barely even concsious at this point.

1b2. The Tree Reflections in the Decision Chamber

Then there is the unusual case of trees being visible in the reflections of the decision chamber. Some people were claiming to see these and some resourceful fan ripped the cube map (image used to create the reflections) to check. Sure enough there they are -

And this is what they look like when seen in game -

So what does this mean? Well it can only mean one of two things as far as I can tell.
  1. At some point Bioware intended there to be trees in this section but removed them. However they forgot to remove them from the reflections.
  2. Bioware intentionally left the reflection of trees in this section to both reference Shepard's dreams and as a clue that this is a dream-like-state.
Interestingly this area is refereed to as the "Guardians garden" in the leaked script. Could it be these were originally going to be in this scene? Whether these trees were ever meant to be part of the scene or only a reflection, it does seem to be a pretty big intentional clue that this scene is directly related to Shepard's dreams.

When you have trees from Shepard's dreams and the boy from them, you have to think there is an intentional link.

The Best Counter-Argument

Bioware made a mistake, the trees are there by accident. Maybe originally the "Guardians garden" was more garden like, and the connection to the dream is merely a coincidence.

1c. The Choices

This to me seems to be one of the more obvious clues to the likelihood of Indoctrination. The Catalyst offers Shepard 3 choices to "end the cycle". It surely cannot be a coincidence that of the three choices two of them were previously proposed by people who were Indoctrinated.
  1. Control - The Illusive Man's choice. A decision we know he was led to during his Indoctrination. We also know that a group of Prothean's also believed the Reapers could be controlled and they turned out to be indoctrinated too. Of course the Catalyst assures us that Shepard could actually control the Reapers for real this time.
  2. Synthesis - Sounds very close to Saren's choice. At the end of Mass Effect 1 Saren talks about how we can avoid being destroyed by the reapers by joining with them. To quote "organic and machine intertwined, a union of flesh and steel. The strength of both, the weaknesses of neither. I am a vision of the future, Shepard. The evolution of all organic life. This is our destiny". Almost exactly how the Catalyst tries to sell Synthesis to Shepard.
  3. Destroy. Shepard's choice. At least up until this point.
So we have two choices that keep the Reapers alive and are also known as arguments the Reapers have used to slowly and subtly Indoctrinate beings in the past. While the final choice destroys the Reapers.
The argument that this is an attempt at Indoctrination and that Shepard's only resistance to the Indoctrination is to choose Destroy seems pretty strong.

Also the Catalyst does his best to paint the Destroy option in the worst light, not only will the cycle continue and we will be doomed to repeat our mistakes and be destroyed by Synthetic life in the long run. But it will kill all Synthetic life existing now, essentially committing genocide against the Geth and killing EDI too.

And not only that, he up's the ante even more by saying even Shepard is partially Synthetic. Strongly Implying that Shepard will die along with anyone else that has Synthetic implants they rely upon to live.

However we know for a fact that the Catalyst is lying here. Not only can Shepard survive with enough EMS but if she was one of your most used squad mates*, EDI can emerge from the Normandy.

Also if this is not strong evidence that two of these choices represent some form of Indoctrination attempt, then why is it that only with the Destroy option (the one we are told is the worst) can Shepard live?

* We do not know for sure but this is the favored theory as to what decides which squad mates step of the Normandy at the end.

The Best Counter-Argument

If Destroy is the "Best Ending" and the other two options are giving in to Indoctrination, why is it that Destroy is the only option you get with very low EMS? Even though Shepard cannot live with such low EMS (and Earth is destroyed) why is it you can not only still resist Indoctrination, but resisting is your ONLY choice?

Wouldn't it make more sense that Shepard would be unable to resist Indoctrination if that is what was going on?

Source - Worst Possible Ending

Or is it that with such low EMS even Destroy is giving in to Indoctrination simply because Shepard dies and Earth is destroyed (at least in Shepard's mind, giving way to despair?).


Could it be that the reason you have such low EMS is because you did not do most of the side missions, meaning you rushed through the game. Meaning the Reapers had less chance to Indoctrinate you?

Or maybe with such low EMS you are going to lose the battle against the Reapers anyway, so they don't really care if you are successfully Indoctrinated. They have already won.

And finally it turns out that having real low EMS does not always mean you can only choose destroy. If you chose to save the Collectors base at the end of Mass Effect 2 and imported that save then Control is your only option -


1d. The Breath

With a high enough EMS when choosing Destroy we are treated with a final cut-scene before the credits that shows Shepard "wake up" and take a deep breath. Revealing that Shepard is alive and has survived.

I have already mentioned the fact that this takes place only after choosing Destroy is a good argument for some element of Indoctrination. But there is another reason this scene adds considerable weight to the Indoctrination argument.
Concrete Rubble in London where
Shepard is hit by Harbinger's beam
Why is it that Shepard appears to be lying among concrete rubble? If Shepard is waking up on the Citadel then why were sections of a space station constructed by such advanced civilizations made with such a primitive material? Surely a space station would be made of light materials. It certainly all appears to be metal at every other point in the game.

One version of The Indoctrination Theory argues that Shepard is actually waking up in London after surviving Harbingers laser and having dreamt/hallucinated everything else as part of a a heightened Indoctrination brought on by Harbingers presence.

This makes sense insofar as London is a place where concrete is not only common but concrete rubble and rebar looking almost exactly the same as that seen in their scene can been seen all over those final parts of the game.
Concrete Rubble with rebar in London
More Concrete Rubble with rebar in London
Shepard surrounded by Concrete in the "breath" scene
If Shepard wakes up in London then it seems logical that Shepard was never on the Citadel and all that was a dream/hallucination. And we SEE the Citadel explode! If it's supposed to be the Citadel then how the hell are we supposed to believe Shepard survived that?

How does Shepard survive this?
Male Shepard Breath Scene

Female Shepard Breath Scene

The Best Counter-Argument

It certainly could be that some parts of the Citadel ARE made of concrete and what appears to be rebar is actually the cables from the Citadel.

The cables in the Citadel and Decision Chamber look very much like what is being claimed to be "rebar".

Cables in London? Or rebar?
And the rebar/cable looks a lot like the cables from the Reaper tech Legion was plugged into. So it could just as likely be cables as rebar.

Also someone used a hack on the PC version to activate a flycam in the Decision Chamber that was able to identify not only similar cables but something that has grooves on it that bares a strong resemblance to the grooves on the concrete in that final scene.

See that video here.

Cables in the Decision Chamber
Concrete like material with grooves
Similar groove seen in concrete in the "breath" scene
Just because it seems unlikely that a space stain has no concrete on it, doesn't mean it doesn't. Also just because it looks like concrete doesn't mean it is.

What is this?
Also what is this thing? Not the concrete rock at the front but the shiny fabricated object behind it. It looks like something that would be found on the Citadel but I have been unable to find an exact match. Or maybe it's part of one of the Alliance vehicles that charged the beam? If we can identify it we may be able to put this mystery to rest at least.

I myself have noticed it bares some similarity to the "Beam Structure" but have been unable to find an exact match. Someone over at BSN made this comparison image which also includes a good comparison of the other strange object to an overturned Macko.

Conclusive? Not at all, but the most compelling identification so far.

2. Other Compelling In-game Evidence That Support's Indoctrination

2a. Choosing Synthesis or Control turns Shepard into a Husk with Illusive Man eyes? (Rel. 1c)

High resolution version of image here. (Note: Can't find original source for this image)

Why is it when choosing either Synthesis or Control, Shepard is seemingly turned into a husk? This could be good evidence that these two option are in effect Indoctrination. Being turned into a husk is well established as a form of advanced Indoctrination. One in which all higher mental functions are lost.

And why does Shepard's eyes turn into ones that match those of the Illusive man?

It is revealed in the 4 part Mass Effect comic "Evolution" that during the First Contact War the Illusive Man was exposed to ancient Reaper artifact on Shanxi that caused this change in his eyes.

Others that were exposed to this activated Reaper relic were turned into a fully indoctrinated form much like a husk. The Illusive Man only came partially into contact with it while saving a friend and was able to escape with less severe changes. The main one being this change to his eyes, the other being an ability to read the glyphs written by the other husks-like creatures.

The Illusive Man says that the artifact is "a booby trap. It's creators planted it to alert them to the presence of advanced species - and to transform them into something they could control."

So it would seem that The Illusive Man's eyes were given to him by being exposed to Reaper tech that was used to Indoctrinate people.

This gives weight to the argument that what is happening to Shepard when choosing these options is indeed part of the Indoctrination process.

The Best Counter-Argument

Shepard's eyes can turn into something that looks a lot like that if going full Renegade, so it may not be a clue to anything other than Shepard having synthetic eyes.

And the Catalyst did say Shepard would die with those two options. It might appear that Shepard is being turned into a husk but is merely just dying in a way consistent with Reaper tech.

2b. Shepard, Anderson and the Illusive Man

I have mentioned how the scene where Shepard meets the Catalyst is the most dream like, but there is plenty of strangeness leading up to that part too.

First of all when Shepard wakes up from being hit by Harbinger's laser all your weapons are gone. However conveniently you find what appears to be Anderson's gun. So where is Anderson? How come he dropped his gun by Shepard but is nowhere to be seen, even though he is going to follow Shepard into the beam soon.

And Anderson is referred to in the subtitles as plain "Anderson" prior to being hit by the laser and "Admiral Anderson" afterwards.

UPDATE: Apparently this change between "Anderson" and "Admiral Anderson" happens several times in the game. So probably meaningless. So focus on the gun in these images.

But the gun change gets even stranger. "SS2Dante" posted in the comments here -

"I noticed when examining the game files that in the red ending files for both the carnifex AND predator are loaded, while in the green and blue only the carnifex is loaded. The carnifex is the gun Shepard used when shooting Mordin, so is presumably associated with negative outcomes/bad situations. Meanwhile the predator is the gun TIM takes from Anderson, and Shepards usual gun. 

Anyway, if you choose Red ending, at the VERY last second, when the explosion occurs, you can see that Shep is no longer holding a carnifex but a predator. "

So if you choose the Destroy ending, it appears the gun changes from the Carnifex to the Predator!

I will use SS2Dante's own thoughts on what this possible intentional symbolism means.

"The gun, I believe is a sign of rebellion. You use it to activate destroy, while in both control and synthesis you toss it away. The first thing you see upon awakening after Harbingers attack is the gun. but each"step" into the dream removes focus from it. When you wake up after the conduit you have to walk forward and "find" the gun on the floor, and when you're talking to the Catalyst you're holding the gun (observe sheps trigger finger in place) but it's invisible."

I took screen shots myself to verify from a video of the ending someone else posted to youtube!

Here is another shot from another source -

And here is Shepard holding the "invisible gun". Note the trigger finger -

Then there is how strange the corridors are on this part of the Citadel and why they resemble the Shadow Brokers ship and the Collector's ship. Is this the art department being lazy and reusing assets? Or is it because Shepard is constructing these area's based on memories of other things? This would also go some way to explaining the "1M1" writing (see 3c) in an area that no organic has ever been, least of all one that can read human English!

Then there is all the strangeness with Anderson being nowhere to be seen after being hit by the laser, but he claims to follow you into the beam. Then comes out somewhere else, seems to see completely different things to Shepard and some how manages to reach the panel before Shepard. And Anderson appears to be unharmed in anyway, even though he has lost all his weapons?!

Then when Shepard and Anderson are confronted by the Illusive Man. The Illusive Man appears to control both Shepard and Anderson. Under the Illusive Man's control, Shepard is made to aim the gun at Anderson. During this oily shadows can be seen around the screens edge. The Rachni queen mentioned "songs the color of oily shadow" in reference to Indoctrination.

Also alien voices, whispers and Reaper sounds can be heard too, very much like those described in the Codex and in Shepard's dreams.

I think we can be certain that what the Illusive Man is doing to control Shepard and Anderson is related to  Indoctrination. And while there is no precedent of anyone controlling another person in such a direct way as to make them aim a gun at someone against there will. The oily shadows and alien voices should be seen as proof that Shepard is the victim to a form of Indoctrination at this point.

When the Illusive Man makes Shepard aim the gun at Anderson, Anderson also raises his hand to mirror Shepard but has no weapon. Then the Illusive Man makes Shepard shoot Anderson in the left side of his stomach. The same place where Shepard has been clutching since waking up from being hit by Harbingers laser.

Anderson clutching his wound
Then after more attempts to convince the Illusive Man he is wrong and has been Indoctrinated, the Illusive Man stands behind Anderson and appears to take a gun from behind Anderson.

This is especially weird because: -

a. The gun he takes is NOT Anderson's gun. Shepard appears to have that.
b. Anderson does not appear to have a gun anywhere upon him earlier in the scene.

Anderson does not have a gun on his back
Maybe the Illusive Man brought the gun himself? Well he also does not appear to have a gun at any other time in the scene. And nowhere to hide it either! Interestingly the gun the Illusive Man producers from who-knows-where is a Predator model. The very same model Saren used when Shepard was able to convince him to shoot himself! Coincidence? Or is Shepard pieces this together from memories?

Finally either Shepard shoots the Illusive Man or convinces him to shoot himself. Either before or after the Illusive Man shoots Anderson.

Shepard walks over a fully flat platform
Shepard walks over to the control panel and opens the Citadel's arms. Then if Anderson is alive he goes and sits beside him or by himself. Here's what's strange with this, Shepard and Anderson sit against a raised platform that was not raised merely seconds ago. Why did it raise up? So Shepard and Anderson had somewhere to sit? Did opening the Citadel arms raise it? Why?

Mere seconds later the center circle has raised so they can rest against it!
Then after they have a chat and Anderson appears to die, Shepard looks down and appears to have a wound that is bleeding profusely in the same place that Anderson was shot.

If there is no relevance to this then why show it? If it's just to show us how injured Shepard is, surely it's unnecessary. We have been controlling Shepard stumble about since the laser, we understand Shepard has seen better days!

The Best Counter-Argument

Again the best counter arguments to most of this is bad writing. Shepard was previously holding that same area to Anderson being shot so maybe the fact the wound is the same place is a coincidence?

The magically appearing gun again could be poor writing or the art department forgetting to give Anderson a gun before that point. And it's not the first time a gun has appeared from nowhere in Mass Effect.

2c. The Dreams: Ghostly Presences,  Oily Shadows and Alien Voices (Ref 1a)

As mentioned before there are three dream sequences in the game. These dreams seem to contain several clues that they are related to Indoctrination.

Ghostly presences made from oily shadows

First Dream Sequence: Shepard chases the boy, who is laughing through a foggy woods. Once Shepard catches up to the Boy a Reaper is heard and they are both bathed in red light. The boy runs away and the Reaper light and noise is gone. When Shepard catches up with the boy the second time he looks at Shepard with a sad face and is engulfed in flames.

Second Dream Sequence: Shepard approaches a bench where the boy is sat that is surrounded by ghostly presences that are made of oily shadows! Shepard also hears whispers presumably from the oily shadows, some of them call Shepard's name. When Shepard reaches the bench the boy is lit by a Reapers red light and the Reaper horn is heard, the boy runs. Wrex can be heard saying Shepard's name (not sure if this only happens if Wrex is dead for you). Shepard reaches the big again, cue the Reaper light and horn, the boy flees again. The whispers increase. Once Shepard reaches the boy he is again engulfed in flames.

Third Dream Sequence: More ghostly oily shadows and whispers calling Shepard's name. Now the child runs from Shepard right away, and there is no more laughing from him. Wrex and Mordin can be heard calling for Shepard (again not sure if this only happens if they are dead). Shepard reaches a clearing and looks on, seeing the boy run into the arms of another version of Shepard, this version of Shepard looks up and smiles back at Shepard and so does the boy. They are both engulfed in flames.

The ghost like presences, oily shadows and alien voices are all consistent with Indoctrinaton.

Many people have spent time trying to figure out some of what the whispers in the dream say. And while none of these are "confirmed" because they are very hard to hear for sure. Here are some lines that people claim to be able to hear -

"don't trust him"
"Get back commander"
"Someone outside is coming"
"Stay away from him, trust yourself"

You can try and hear some of them yourself here.  And here.

But most telling of all, when Shepard wakes up from any of the dream sequences the screen is bathed in a white light as a transition showing the movement from dream to reality. Here is a screenshot -

It's also the same dissolve when Shepard exits the Geth Consensus and when entering the beam. Here are some comparison frames showing this.

Geth Consensus
Getting hit by Harbinger's Laser / Entering the Beam / Rising platform to the Catalyst
Is it merely a coincidence that the transition dissolve Bioware chose to use after Shepard is hit by Harbinger's laser is the VERY same one used to symbolize a transition from a non-reality to reality?

I think this alone is VERY strong evidence that Shepard is dreaming at this point.

The Best Counter-Argument

Sorry but the only counter argument I have seen to these points are that they are all merely a coincidence. If anyone has anything better please let me know.

Of course the whispers are mere guess work, they are very hard to hear.

2c. The Plot Holes, strangeness and Illogical Story Elements

There seems to be a rather massive amount of elements in the final 20 minutes or so of Mass Effect 3 that just don't make a lot of sense. The fact that many of these problems go away if you view them through the lens of the Indoctrination Theory seems to add more credence to it being true. It could be that many of these are explainable, or that the Extended Cut will fill in the gaps that make them make sense. But it could also be that they are all small clues to a bigger picture.

Here is a list of things that seem to be explainable if Shepard is in large part hallucinating/dreaming everything after being hit with the beam. But taken literally seem to not make much sense at all.
  • Why is it that after being hit by Harbinger's laser Shepard wakes up CLOSER to the beam than when hit? Surely it would have knocked Shepard backwards not closer!
  • Why is it that after waking up and beginning to stumble towards the beam Shepard hear's this -
Marine: Did we get anyone to the beam?
Major Coats: Negative. Our entire force was decimated.
Major Coats: It’s too much. We need to regroup. Fall back to the buildings…
Marine: Hammer's wiped out. All forces, retreat.
Marine: Pull back! Pull back!
Is Major Coats simply unable to see Shepard and Anderson still stumbling towards the beam?
And based on the final cut scene with the Normandy the two other squad mates that came with Shepard were also alive!

How the HELL did our squad mates survive Harbinger's laser and get back on the Normandy seemingly unwounded in any way? I'll come back to this in a moment.
  • How is that when Shepard looks around when stumbling toward the beam there is no sign of Anderson who claims to "follow" you into the beam?
  • What is with these strange bodies by the Mako before the beam -

They were not there before Shepard got hit with the laser. And they seem to bare a strong resemblance to Ashley and Kaiden in Mass Effect 1. Except they are bald, making them look more like dolls.

Are they supposed to be a manifestation of Shepard's guilt at not being able to save everyone? Since one of these two dies in ME1 and the other was seriously injured at the start of 3. Or are they simply meant to show that a lot of people have died trying to get to the beam? Or have been collected by the Reapers and placed by the Beam? If so why is there thousands of them and they all look the same? And why do they look so crap? Did the art departed really become that lazy at this point and just mapped a crap texture of two dead humans onto some low polygon piles to show all this sea of corpses? Why? What is so important about them to even bother? If you were not going to make them look good why not just leave this area how it was BEFORE Shepard is hit by the laser?
  • Why does Shepard lose all weapons? Why does Shepard find what appears to Anderson's gun on the floor after waking up? Where is Anderson at this point? Since Anderson does not appear to have a weapon when you reach the control panel it certainly seems he dropped his somehow besides Shepard while also not being anywhere in sight and then "following" Shepard into the beam?
  • Why is it this new gun Shepard picks up does not need to be reloaded and never runs out of ammo?
  • Why is Anderson referred to as "Anderson" in the subtitles before being hit by the laser and "Admiral Anderson" afterwards?
  • Is there any significance to the trees around the beam area? They seem very unusual after Shepard is hit by the beam.
  • Why is it that this new section of the Citadel bares many architectural similarities to the Normandy, The Shadow Brokers ship and the Collectors Base? 
  • Why is the corridor leading to the control panel full of dead bodies? Also note they do not resemble those by the Mako except they are also bald and doll-like. They are however fully rendered models not a terrible 2D texture. Were they all brought there after being killed? Why? If they have a purpose then why are they so strangely scattered?
  • Why are there Keepers in the corridor working on "invisible" control panels?
  • Why does Anderson come out of the beam at a different place to Shepard?
  • Why does Anderson reach the control panel before Shepard after entering the beam afterwards?
  • Why does Anderson mention moving walls that Shepard never sees?
  • How is it that the beam takes Shepard and Anderson to a place where they only need to walk through a few corridors and they are exactly where they needed to be? At a control panel that opens the arms. If the beam was being used by The Reapers to transport humans to the Citadel for the supposed purpose of making another Human Reaper, where are the Reaper forces working to do that? Why do the Reapers have the transport beam open at all if no Reaper forces are using it? When Shepard and Anderson get there all they find is dead bodied, Keepers that appear to be doing nothing and a path leading directly to the control panel to open the Citadel arms thus leading to the failure of the Reapers plans! None of this makes any sense
  • Where does the Illusive Man come from? How did he get there? Also we are told that the Reapers moved the Citadel to Earth because the Illusive Man who is Indoctrinated told them it is the Catalyst. Why then does he still believe he is working against the Reapers until Shepard is able to convince him otherwise? When Saren was Indoctrinated the Reapers had promised he and others would be spared by Synthesis but it seems unlikely that the Illusive Man would have believed the Reapers would just let him control them.
  • Why can the Illusive Man (who has at this point clearly very Indoctrinated), control Shepard and Anderson's movement? There is no precedent in the games before this that anyone could have this ability.
  • Where does the Illusive Man magic a gun up from? He appears to take it from Anderson but Anderson did not have a gun at this point.
  • Why is it that if Shepard is successful in convincing the Illusive Man to resist his own Indoctrination, Shepard only needs 4000 EMS (rather than 5000) to "wake up" alive after choosing Destroy? You may argue that without the Illusive Man Cerberus are less effective which helps Shepard's Effective Military Strength. But if that was the case then why is it not given as an additional 1000 EMS to contribute to saving Earth too? Rather it is given as needing less EMS to "wake up". Note: It has been claimed is is actually if you prevent TIM from killing Anderson that you only need 4000 EMS to wake up. If Anderson represents Shepard's will to fight Indoctrination this adds more weight.
  • Why does Hackett contact Shepard out of the blue, with no prior contact since Major Coats claimed everyone was dead and know Shepard is alive and was the one that opened the Citadel arms? Why did Hackett not try and contact Shepard before this point? Not even to say "Shepard!? Are you there? Was it you that opened the Citadel's arms?"?
  • Why was Joker running from the flight? Is it that after Major Coats reports that everyone is dead, he swings by to pick up the squad mates (who inexplicable are on the Normandy at the end), although nobody bothers to look for Shepard and as soon as Shepard activates the Crucible he see's the resulting wave and is quick enough to almost outrun it?
I said I would come back to this, so here it is. The fact that Shepard's squad mates that were either fighting on the surface of London or part of the assault on the beam in which everyone was "decimated", turn up unhurt and on the Normandy is one of the biggest offenders in those final scenes. As far as I can tell everyone hates the lack of logic or explanation here.

Even if we conclude that while Shepard was unconscious on the ground the squad mates were picked up, we have to ask why they left Shepard. If we conclude that our Squad mates retreated (very out of character), why did they do so while so unharmed? Maybe they were picked up while Shepard was passed out again on the Citadel (Shepard may have been unconscious for an unknown amount of time after dealing with the Illusive Man and speaking to Anderson)? But why would they not continue the assault on the beam? Even if they thought Shepard was dead, anyone should be able to complete the mission. Why give up? Especially when Harbinger retreats!
  • And by some miracle the Normandy crash lands on some utopian looking planet with a perfect atmosphere for life? How many are those in the galaxy anyway? What are the odds?
What about the things the Catalyst claims? Evidence it's all part of an Indoctrination attempt? Or is the Catalyst simply lying to Shepard?
  • The idea that organics being protected from being wiped out by synthetics by being periodically wiped out by some synthetics makes very little sense. And is very unconvincing as the Reapers overall motive. It's at best deeply flawed circular logic. The Catalyst would have us believe that Synthetics are destined to wipe out their creators, and finally all organic life. But not only does this contradict the lessons we learned from the Geth/Quarian conflict but there is no basis of evidence to support the notion that Synthetics are destined to want to wipe out all organic life at all.
Let's consider this. If all Synthetic life had to have been created by organic life by it's very definition. And the Reapers are Synthetic, then why did the Reapers not wipe out all organic life? The Catalyst offers us nothing more than contradictory circular logic.

In order for it to be true and explainable it would require massive presumptions that are not offered or hinted at in the game. At the very least this would be appalling storytelling. Something Bioware do not have a history of.
  • Why is the Catalyst's "solution" proven not viable anymore simply because an organic made it to the control panel on the Citadel? Or is it simply because we were able to complete the Crucible? What does either of those have to do with the claimed inevitable synthetic genocide against organics?
  • If the Reapers created the Citadel why did they bother to even create the Decision Chamber along with appropriate places for someone to "Control" or "Destroy" them? Did they foresee organic life building the Crucible and eventually making it there and wanted to provide them the options? 
  • Why is it that despite the claim that the Destroy option will kill all synthetic life along with Shepard because of being "partially synthetic", both Shepard and EDI can be seen alive afterwards?
I'm sure I will add a lot more to this list later when they occur to me or people point them out but for now I think you can see there is enough to have some serious questions about the ending. Indoctrination Theory does help answer most of these by claiming most of it is a dream/hallucination and the illogical nature of a lot that happens is because of that.

Here is another excellent document breaking down how the ending makes no sense in a logical interpretation.

The Best Counter-Argument

Unfortunately while I could list possible explanations for all these inconsistencies they all still add up to the point that they are ridiculous and require far too much suspension of disbelief to accept the explanations.

The most common and seemingly strongest overall argument against any of these things supporting an Indoctrination Theory is simply that Bioware wrote a terrible ending that doesn't make sense. There is no hidden meaning, it's simply crap writing.

3. Clutching at Straws 

Ok so we have seen some rather compelling evidence to support the notion that Bioware fully intended an element of Indoctrination to be a viable interpretation of the ending.

If this is true we would expect to see lot's of other subtle clues throughout the game. After all we are led to believe that the ending was mapped out really early in the development cycle.

As it happens, fans have pointed out a lot of very interesting things that certainly could be clues of Indoctrination. However taken alone these things are not very convincing and IT-debunkers like to focus on these things as proof that IT-believers are "clutching at straws".

So let's be clear here. These things are being pointed out so that taken as a whole they can be seen as really cool possible clues that add weight to the possibility. They are not being presented as single pieces of evidence that offer any form of singular proof.

3a. The Similarities With the London Street and The Decision Chamber

As the theory goes, Shepard is in fact still unconscious (or-semi-conscious) on the street of london at the approach to the beam. So it's very interesting to note that there are some striking similarities between elements of the approach to the beam and the decision chamber, as seen below. Mere coincidence? It certainly could be.

3b. The Boy Next to Warning Signs

Another very interesting thing that has been pointed out is the fact that several times when Shepard see's the boy alive he is next to some form of warning sign. A warning from Shepard's mind or another coincidence?

It's also worth noting that the Warning sign in the duct seems to be unique. Not only is it an unusual symbol to warn against an electrified duct (a lightning bolt to the brain?) but if it appears nowhere else in the game, does it not seem likely that Bioware very intentionally placed it here with some purpose?

3c. The Locked Door and the Boy

Upon approaching the room where Shepard see's the boy in the duct, you can actually see the boy on a balcony outside the room. He appears to see the Husks coming and runs into the room behind him. However the door is clearly locked and does not unlock to allow him to enter. It simply opens for him while remaining locked. Simply a bug or a clue?

3d. The 1M1 signs in the Citadel

Here is one that I have now discounted.On the ramp to the panel in the Citadel and in the entry to the decision chamber there are several places where a sign that reads "1M1" can be seen. And the sign is mirrored on the opposite side as seen above.

Two interesting things about this.
  • First of all why is there writing on a part of the Citadel that was built by the Reapers and no other organic has ever been!?
  • And why is it written in Human English!?

At first I could only think of two explanations for this.
  1. Bioware intentionally placed it there as a clue to something.
  2. Bioware are lazy and used an art asset on the Citadel that was supposed to be for Human structures.
If the first one is true then what does it mean? Well some fans put forward some rather amazing theories on that. It get's a bit technical so I'll leave the link here for a full explanation. But here are some very interesting highlights.

1M1 is actually a formula for dioptry, or inverse focal length (convergence)

Convergence has 3 definitions...

1: The act of moving toward union or uniformity.
2: A meeting place.
3: The intersection of three electron beams for red, green and blue onto a single pixel in a CRT.

Or could it be that like the similarities between this part of the Citadel the Shadow Brokers ship and the Collectors ship, this is a clue that Shepard is constructing these places from memories of others places?

However since this same graphic can clearly been seen in places when climbing the Citadel tower in Mass Effect 1 -

Mass Effect 1, climbing the Citadel tower with Sovereign in the background

There is clearly a third option why this could be there.

  • Because it is already an established visual from the Citadel tower in the first game and Bioware were maintaining visual continuity despite the fact that it lacks logic.

So I think we can discount the dioptry formula connection as coincidence. There is no way that was planned from the first game.

And while it remains a mystery why human English is used on a structure that was supposedly built by the Reapers, it does seem that it's inclusion in the ending is meaningless.

3e. The Trees Around the Beam

A lot has been made of the trees scattered around the beam after being hit by Harbingers laser and if they relate to the trees in Shepard's dreams. And while this was once offered as one of the main pieces of evidence for Indoctrination I originally chose not to include it simply because it has been shown that there are many trees around that area even before Shepard is hit with Harbinger's laser.

However prettz over at the Bioware Social Network Forums took these screenshots which I think serve to reignite this point as legitimate evidence.

Before Shepard is hit
After Shepard "waked up" from being hit by Harbinger's laser
As you can see there are clearly trees and shrubs where there were none before. And you have to ask, why would Bioware remodel this area for after Shepard wakes up? There really is no reason to have a separate model map for this area with new trees in it. You don;t need to do that to add some flipped over Macko's.

You don't even need to do that to add those weird piles of bodies mentioned in 2c. So what possible reason could Bioware have for adding trees into this area at this point if not to make everything strange and dream-like and as a call back to the trees in Shepard's earlier dreams?

3f. Feelings of Being Watched and the Hum

The Codex entry on Indoctrination mentions "feelings of being watched" and "buzzing or ringing" in a persons ears.

So it is interesting that in the game James mentions a strange hum. I can't recall if it was more than this one time but it's a strange comment, possibly a clue?

There also seems to multiple times in game where characters make reference to being watched. James on the fuel station mission says "Yeah, I feel like we're being watched.". Tali on the Rachni mission can say "It feels like we're being watched. Let's find the nest and get out of here.".

These could easily be coincidences and it's worthy of note that if Shepard were the one being Indoctrinated, then it should be Shepard that mentioning the feelings of being watched and the hum.

3g. Interesting Comments Made in Game that refer to Indoctrination

After Ashley's encounter with Udina, and you meet her before returning to the Normandy, this dialogue takes place:

Ashley: "I can't believe he was responsible for all of it. Was he indoctrinated?"
Shepard: "It's hard to say."
Ashely: "How do we fight something that can worm it's way into your head?"
Shepard: "I don't know. But we don't have a choice."
Ashely: "No we don't."

On Thessia, when you are trying to recover the Prothean VI:

Liara: "This nightmare never ends!"
Shepard: "The hell it won't! We get to this artifact, and we can all wake up."

If you bring Garrus: "Drinks will be on me."

4. Evidence From Outside the Game

4a. Things found from extracting game files and code

Dream Foliage!

At the end of the game when we see the Normandy crash land on the utopian looking Earth like planet, the Indoctrination theory would have it that that scene is a dream. It simply does not make sense that the crew would be aboard the Normandy or that Joker would run from the fight, or that it would manage to crash on a perfectly inhabitable planet by some miracle.

Could this be Shepard dreaming about a desired outcome? Well digging into the texture files in the PC version some fans stumbled upon this seemingly damming piece of evidence.

This is the textures files from those scenes. We know this not only because we can clearly see they are but  they come from the package "BioA_End003_Planet".

However this same texture IS used in the actual dream sequence -

Note the package this is from is "BioAp1_Lv1_Dream". So evidence completely discredited? Well not entirely, there certainly could be some significance to the fact that the same plants are seen in Shepard's dream and the Normandy scene that might be a dream/hallucination.

However it is just as likely that these texture assets were created for the actual dream sequence and then reused for the Normandy scene.

End Choice Bad

Another interesting discover is that the model for the Control endings pillars is named "End_Choice_BadA_01". So presumably the artists that created these was at least of the opinion that the control ending was bad.

Reaper Indoc Effects

Here is another interesting find. BSN forum user Giskler found this in the files related to the Illusive Man showdown.

You might need to click to enlarge to read this but what we believe it is, is the files related to the effects seen on screen (the blur and oily shadows) when the Illusive Man is seeming to control Shepard and Anderson. The files names seem to suggest someone else is behind this control -


That's right they are Reaper Indoc effects.

Plot ID's in Save Game Data

A poster (Leto_Galt) on the Bioware Social Network found this interesting gem...

I was looking through some save game editing plot flags and noticed that the line for End001 (Destroy) is different than End002 and End003. Destroy Sets 3 PlotIDs for the future.Not only do Synth and Control not set 3Ids. They do not even set 1.




I don't understand exactly how the game engine uses these PlotIDs, but from a layman’s point of view it looks like it's either;
Pick destroy, and have a future, or Synth/Control and not have a future.
Bioware does not even bother to track which one you picked if it wasn't destroy.
As far as they are concerned synthesis & control are the same thing. = Indoctrinated.

UPDATE: It seems that "End001", "End002" and "End003" actually refer to the section of the ending, rather than each ending choice. So this could also have no meaning I have yet to confirm but will update if this because proven.

Become a Reaper

If there was any doubt that Control is a bad ending, this snippet of code describing the different endings should clear it up. According to these lines of code, choosing Control means you are choosing to "Become a Reaper"!



4b. Comments Made by Bioware That May Help Clarify the Endings and Their Intent

Interview with Casey Hudson (Director) 03/12/12

“I didn’t want the game to be forgettable, right down to the sort of polarizing reaction that the ends have had with people–debating what the endings mean and what’s going to happen next, and what situation are the characters left in. That to me is part of what’s exciting about this story. There has always been a little bit of mystery there and a little bit of interpretation, and it’s a story that people can talk about after the fact.”

Bioware intended the ending to be controversial. They wanted us to debate what the endings mean, which suggest to me they intended there to be deeper interpretations other than the littoral one. I doubt they expected as much anger and backlash though. I also doubt they did not expect there to be as much debate afterwards either. Or maybe they did? I certainly did not expect to write a 10,000 word document on the ending!

From the Digital magazine for iPad and PC "The Final Hours of Mass Effect 3"

"Hudson and Walters spent most of their time focused on refining the end of the game, the final hour of Mass Effect 3 that would choreographed down to the second"

If it was choreographed down to the second how could so many illogical things happen during it? Unless all those illogical things are clues?

"How to end the trilogy was another subject of great debate. The massive Illusive Man boss battle was jettisoned, but the team was still unsure how to wrap things up. Hudson was pretty sure he wanted this to be the end of the Commander Shepard story, but did that mean he would die or survive? For weeks Hudson and Walters discussed the emotions they wanted players to feel at the end of the game and then wrote dialogue and scenes to support those feelings. One night Walters scribbled down some thoughts on various ways the game could end with the line "Lots of Speculation for Everyone!" at the bottom of the page. In truth the final bits of dialogue were debated right up until the end of 2011."

So we know they planned us to be speculating this ending. If the literal version was true I don't think it requires as much speculation as questions as to why it's crap.

And the fact they were debating the final bits of dialogue shows how much attention to detail they had. This was no slapped together ending that was rushed with little thought or care.

"And even in November the gameplay team was still experimenting with an endgame sequence where players would suddenly lose control of Shepard's movements and fall under full Reaper control. (This sequence was ultimately dropped because the gameplay mechanic proved too troublesome to implement alongside dialogue choices.)"

I think this quote is VERY important. As late into the development cycle as November 2011 they were working with a gameplay sequence that had Shepard fall under FULL Reaper control, which was removed. Note they did not mention removing a story section where Shepard was under Reaper control, but a gameplay sequence where Shepard was under FULL Reaper control. Suggesting to me that the game still contains that section with Shepard under partial Reaper control.

So Shepard being fully Indoctrinated was a part of the game, for a FACT as late in development as November 2011!

"We appreciate everyone’s feedback about Mass Effect 3 and want you to know that we are listening. Please note, we want to give people time to experience the game so while we can’t get into specifics right now, we will be able to address some of your questions once more people have had time to complete the game."

This says to me there are twists in the plot that they don't want to reveal until more people have played. Would also be a good reason to hold back an ending that exposed these twists until the summer.

4c. Comments Made by Bioware that are Confusing in the Light of the Current Endings

One of the strangest things about the ending, regardless of if Indoctrination Theory is correct or not is how many comments Bioware have made that seem to contradict the ending as it stands now. Could these be clues to what is coming in the Extended Cut? Could it be the original ending was cut out to be used in the EC? If not then why do many of these comments seem like outright lies?

Comments before the game went gold:

Interview with Casey Hudson (Director) 4/28/11

“For people who are invested in these characters and the back-story of the universe and everything, all of these things come to a resolution in Mass Effect 3. And they are resolved in a way that's very different based on what you would do in those situations.”

Interviewer: [Regarding the numerous possible endings of Mass Effect 2] “Is that same type of complexity built into the ending of Mass Effect 3?”

Hudson: “Yeah, and I’d say much more so, because we have the ability to build the endings out in a way that we don’t have to worry about eventually tying them back together somewhere. This story arc is coming to an end with this game. That means the endings can be a lot more different. At this point we’re taking into account so many decisions that you’ve made as a player and reflecting a lot of that stuff. It’s not even in any way like the traditional game endings, where you can say how many endings there are or whether you got ending A, B, or C.....The endings have a lot more sophistication and variety in them.”

“We have a rule in our franchise that there is no canon. You as a player decide what your story is.”

“Every decision you've made will impact how things go. The player's also the architect of what happens."

Whether you're happy or angry at the ending, know this: it is an ending.
BioWare will not do a "Lost" and leave fans with more questions than
answers after finishing the game, Gamble promised.

“You'll get answers to everything. That was one of the key things. Regardless of how we did everything, we had to say, yes, we're going to provide some answers to these people.”

“Because a lot of these plot threads are concluding and because it's being brought to a finale, since you were a part of architecting how they got to how they were, you will definitely sense how they close was because of the decisions you made and because of the decisions you didn't make”

"Of course you don’t have to play multiplayer, you can choose to play all the side-quests in single-player and do all that stuff you’ll still get all the same endings and same information, it’s just a totally different way of playing"

NOTE: The problem with the above quote is that it seems almost impossible the get the "perfect" ending with Shepard surviving with only the single player.

“And, to be honest, you [the fans] are crafting your Mass Effect story as much as we are anyway.”

Comments made after the game went gold. So no changes could be made at this point. The ending on the disk, was set in stone (or digital versatile disk if you will).

“Experience the beginning, middle, and end of an emotional story unlike any other, where the decisions you make completely shape your experience and outcome.”

“There is a huge set of consequences that start stacking up as you approach the end-game. And even in terms of the ending itself, it continues to break down to some very large decisions. So it's not like a classic game ending where everything is linear and you make a choice between a few things - it really does layer in many, many different choices, up to the final moments, where it's going to be different for everyone who plays it.”

“There are many different endings. We wouldn’t do it any other way. How could you go through all three campaigns playing as your Shepard and then be forced into a bespoke ending that everyone gets? But I can’t say any more than that…”

“[The presence of the Rachni] has huge consequences in Mass Effect 3. Even just in the final battle with the Reapers.”

“Fans want to make sure that they see things resolved, they want to get some closure, a great ending. I think they’re going to get that.”

“Mass Effect 3 is all about answering all the biggest questions in the lore, learning about the mysteries and the Protheans and the Reapers, being able to decide for yourself how all of these things come to an end.”

Interviewer: “So are you guys the creators or the stewards of the franchise?”

Hudson: “Um… You know, at this point, I think we’re co-creators with the fans. We use a lot of feedback.”

“I’m always leery of saying there are 'optimal' endings, because I think one of the things we do try to do is make different endings that are optimal for different people”

Interview with Mac Walters (Lead Writer) 3/7/12
Issue 108 of 360Gamer (Hardcopy only, not available online)

When asked about the science of the game being plausible

"From very early on we wanted the science of the universe to be plausible. Obviously it's set in the future so you have to make some leaps of faith but we didn't want it to be just magic in space."

I believe this is the source of the term "space magic".

“The whole idea of Mass Effect3 is resolving all of the biggest questions, about the Protheons and the Reapers, and being in the driver's seat to end the galaxy and all of these big plot lines, to decide what civilizations are going to live or die: All of these things are answered in Mass Effect 3.”

4d. Twitter!

My goodness Twitter has been a source of great debate around the end of Mass Effect 3, especially the Tweets of Bioware community manger Jessica Merizan and Associate Producer Mike Gamble.

Let's start with the one that I think is most important. On the 8th of March, 2 days after Mass Effect 3's release Mike Gamble (among others) were beginning to feel the full force of Mass Effect fans disappointment at the current endings. It was at this point Mr. Gamble posted this to Twitter -

If this was in direct response to all the anger at the endings (which it clearly appears to be). Then logic dictates that he is suggesting they are planning something with the endings that he believes would remedy why people are hating them. And remember this was long before the Extended Cut was announced! Was an expanded ending planned from the start? Remember this was 2 days after release!

And when another user asked the main Mass Effect Twitter account this -

This was the reply -

So if we knew what was in store we would be less unhappy about the ending according to Bioware! So something was already planned 2 days after release, long before the anti-ending movement even really gained traction. 

I think it is clear from this that they are not talking about any old DLC, but very specific DLC related to what people are upset by. The endings!

It would seem that Bioware always intended to do something that would change peoples feelings towards the endings. If Indoctrination was the intent, then a delayed reveal to allow people time to experience and speculate would not only make sense, it would be brilliant.

It would be one of the best events in gaming of all time! Especially if it was on the back of months of heated debate on the issue. 

More Tweets and analysis coming soon...

5. Problems with Indoctrination & Arguments Against

Make no mistake, juts because I am arguing that the Indoctrination Theory was fully intended by Bioware it does not mean I think there are no problems with it.

It's biggest and most obvious problem to me is the fact that if true we are left without a real ending. We do not know if the Reapers were ever defeated. We do not know what happened to our squad mates or the rest of the galaxy for that matter.

It seems to me that if the Extended Cut is to deal with these issues it almost certainly needs some additional gameplay. Why would Bioware put themselves in a position to be criticized for not releasing a full game?

Or maybe they fully intend to always leave the ending ambiguous. Maybe they simply want us to debate this ending, after all we were never supposed to know if Deckard was really a replicant in Blade Runner. But this seems too much of a cop out. This goes beyond if one man was a synthetic life form, the entire fate of the galaxy is left undecided.

I personally feel that if Bioware leave the ending open to interpretation they will make things worse. The IT believers will feel their story has not ended. And the IT-skeptics will continue to just hate the ending.

Bioware are between a rock and a hard place. I simply cannot see how the literal ending can be saved, it's that bad. Now if it's intuitionally like that because IT is the truth, it NEEDS to be resolved. Bioware lose their artists vision of leaving us all on a brilliant debatable question, but if they don't they lose their artistic credibility because far too many people will continue to believe the literal ending is true, and that's it's terrible.

The percentage of people that seem to like the ending appears to be very small, and virtually none of the hardcore base see to (looking at the forums and polls).

The Prothean VI

Many people have argued that the fact that the Prothean VI identifies Kai Leng as an "Indoctrinated presence" but not Shepard is proof that Shepard is not Indoctrinated.

However the theory is that Shepard is slowly being Indoctrinated and is not already Indoctrinated. And since we know the Prothean's were also infiltrated by Indoctrination, it stands to reason that either their detection skills are not 100% or they can only detect a fully Indoctrinated being.

I'll probably continue to add more poignant criticism of Indoctrination here later.

6. Other Thoughts, Theories & Conjecture

How Long Has The Illusive Man Been Indoctrinated? (Ref. 2a)

Since we know that the Illusive Man was exposed to Reaper tech that was used to Indoctrinate people in the First Contact War can we conclude he has been Indoctrinated since then? Are his actions in ME2 rather odd if already Indoctrinated?

Well we also know that Indoctrination can be a very long and slow process, and it is strongest when within proximity of Reapers. So I think we can guess that he was only in very early stages of Indoctrination up until the arrival of the Reapers in ME3, due to the way he was exposed (see the Mass Effect 4-part comic Evolution).

Many of his decisions were probably subtly influenced by the Reapers since the First Contact war, and once the reapers arrived in ME3 they had laid enough ground work to fully take control of both him and Cerberus itself.

How Similar All the Endings Are

It is very interesting in light of all the talk from Bioware about how dynamic and varied the endings would be to note that there are only actually 6 different endings. Unless you count the differences of who can step off the Normandy as a different ending.

And how remarkably similar all these endings are! Here is a breakdown of what endings you can get.

Destroy Good, Destroy Bad, Destroy Vaporization
Control Good, Control Bad
Synergy Good

See all six endings in action side by side -

Thematically Revolting

Over on the Bioware Social Forum one poster posted the thoughts of their Lit Professor who had played through the game. His outline of why the ending is thematically contrary to the rest of the entire game series is concise and compelling.

I think it adds weight to the discussion of how Bioware could have dropped the ball so massively in the last 20 minutes of there masterpiece.

Read it here.

The Motivations of the Reapers

One of the least convincing things that the Catalyst tells you is the motivation of the Reapers. We are told that in order to preserve advanced organic life from being destroyed by the Synthetic life it created the Reapers to harvest them and preserve them into new Reapers.

I have already gone over the circular and flawed logic of this. Also though, is organic life really "preserved" by being turned into goo that fuels a Reaper? I think not.

And what species was harvested in the first place to make the Reapers? And harvested by whom if the Reapers were not yet made? Too many questions that I am simply going to call it BS.

So what other clues do we have to the Reapers motivations throughout the games.

Well in Mass Effect 2 EDI suggests that the Collectors are 'facilitating Reaper reproduction' by constructing a new Reaper, and also estimated that the Collectors would have to gather millions of humans in order to complete it. EDI also speculated that any Reaper is built to resemble the race used to create it, and that the Reapers had unsuccessfully attempted to construct a Reaper from Prothean raw material.

So if the Reapers are built to resemble the race used to create it, then why do they all look like Cuttlefish?

UPDATE: Well it turns out Mass Effect 3 lead writer Mac Walters claims that it is only the "Core" of the Reaper that assumes the shape of the original species. I have modified my theory to accommodate this. -

[Game Informer] Why do most of the Reapers we’ve seen so far have similar insect-like appearances? The human Reaper looked different, but otherwise it seems like the Reapers mainly build themselves out of bugs. Is that correct?

[Mac Walters]: The exterior of the Reapers does follow a similar pattern, an efficient design for the purpose they were created for. However each Reaper is created from a unique species, and as we saw at the end of Mass Effect 2, the core of each Reaper is designed in the likeness of that species.


If this is true, why? Why do they need to make the core in the shape of the species the DNA goo comes from? It's hardly like the species is better preserved by having that shape, since it is never seen. And anyway the species is actually DNA goo!

If EDI is correct and the Reapers are actually more interested in using advanced organics in order to reproduce, rather than to preserve the organic race that would actually make a lot more sense, as I said would you feel "preserved" as genetic goo?

What they are preserving, is themselves.

Could it be they hide in hibernation waiting for organic races to reach a certainly level at which point they would be most likely to be a suitable match for Reaper reproduction. The Reapers send collectors to test the organics to find the best possible match and once found they emerge to harvest said race and wipe out the others to prevent them warning the future organics.

After all if there purpose was to preserve organic races, why did they fail to harvest the Protheans?

It would explain why the Reapers took a big interest in Humans. Because they believed the diversity of our genetics gave them the best chances at reproduction. 

It would also make sense of what the Collectors were up to, sampling each race ahead of the Reaper invasion to find the most suitable candidates. It would explain why the Human Reaper was being built ahead of the actual Reaper invasion too.

And it would explain why Earth is such a frontline for the Reaper invasion in this cycle.

It is so far the best theory I have come up with.


Be sure to let me know what I have missed or if I have gotten any of the facts incorrect.

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


Credits, Thanks and Acknowledgments

None of this would be possible without the incredible work of a great many Mass Effect fans. I will try and credit and source everyone I have used to put this together. If anyone feels I have missed someone, please do not hesitate to contact me and let me know and I'll be sure to add them.

From the Bioware Social Forum
byne - Was the ending a hallucination? - Indoctrination Theory Thread
Turtlicious - Compiled many theories used in that thread.
kyleh619, Deklan_Caine, Luc0s, Kitten Tactics, lookingglassmind: - Offered theories used in that thread
obie191970 - Boy next to Warning signs images.
balance5050 - Concrete rubble images from London
Rifneno - Feelings of being watched
Johnny G - Comments from Bioware
JTP117 - Dream Diolougue
Gallifreya - Feedback and in game comments that refer to Indoctrination
Sire Styx - Feedback
Rifneno - Feedback and End_Choice_Bad model
llbountyhunter - Feedback and Platform that raises for Shepard and Anderson

prettz - Screenshots of tree's before and after being hit be Harbinger
SS2Dante - Gun change when choosing Destroy

- Shepard's Indoctrination (NEW)
- Mass Effect 3 Ending - Worst Possible Ending
- Female Shepard Breath "Mass Effect 3: Destroy Ending"
- Male Shepard Breath "Mass Effect 3: Shepard Lives! Ending"
- "Mass Effect 3 - Ending Movie Comparison - All the Colors"
 - First Dream Sequence
 - Second and Third Dream Sequence
 - Boy runs through locked door.
Bill Casey, balance5050 - Tree reflections thread

Lone Irbis

Other Videos
MyVids2010 - Mass Effect 3 Indoctrination Synthesis Saren/Reaper's Trick

Other Sources and articles of note