6. Other Thoughts, Theories & Conjecture

How Long Has The Illusive Man Been Indoctrinated?

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 (Pre-EC)

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 - 

The Bizarre Similarities with the Ending of Mass Effect 3 and Mass Effect 1

Why is it that there are HUGE similarities between the events at the end of Mass Effect 1 and Mass Effect 3?

While I am not sure this supports the Indoctrination Theory because part of it begins before Shepard's hallucinations are supposed to begin, it does seem very odd.

Let me explain. Does this sound familiar -
  • Shepard and squad make a mad dash towards the "conduit" a device that will teleport them to the Citadel.
  • Upon reaching the Citadel Shepard searches for the control panel that will open the Citadel arms in order to defeat the Reapers.
  • But before reaching the control panel Shepard has to confront an Indoctrinated antagonist. Shepard is able to convince this person that they are Indoctrinated at which point they shoot themselves.
  • After dealing with this person Shepard opens the Citadel arms using the control panel which enables the Reapers to be defeated.
Everything I described above is an accurate description of both Mass Effect 1 and Mass Effect 3 alike!

Why do they name the Reaper teleportation beam that takes you to the Citadel the "conduit"? The very same name as the Prothean mini relay that takes Shepard to the Citadel at the end of the first Mass Effect?

And why is it that once Shepard reaches the Citadel your goal is the very same goal as Mass Effect 1? 

In the first game you are opening the arms to allow the fleet to enter and defeat Sovereign who has attached himself to the top of the Citadel tower.

In Mass Effect 3 you are opening the arms to allow the Crucible to attach the platform that is the BOTTOM of the Citadel tower. Almost the same location!

Could it be that Shepard constructs these events from memory as I have suggested elsewhere? Although the assault on the conduit takes place before the hallucinations are supposed to begin.

It would explain how odd it is that there is a Citadel control panel in a section of the Citadel that turn out to be the underside of the Citadel tower. That entire sections existence makes no sense. The only way to access it appears to be through the previously non existent conduit. So why is there a control panel at all? Especially one that is accessed by walking a straight line from where the conduit drops you!

It's all very odd and to me it makes it all even more dream like.

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 unlikely it is that Bioware could have dropped the ball so massively in the last 20 minutes of their masterpiece.

Read it here.

Identifying the Planet the Normandy Crash Lands on

I noticed the similarity between the planet the Normandy crash lands on and the planet Zorya from Zaeeds loyalty mission myself but Ravereth, a user over at BSN posted these great comparison images, along with the 2 moon similarity with the horrible post credit "tell me another story of the Shepard" scene.

Did Bioware simply reuse assets from this planet or is this supposed to be the planet they crash land on? If it is then I believe it is two full relay jumps and a system away from Earth. Unlikely they would make it there when running away from that Citadel explosion.

Or could it be Shepard is constructing this planet from memories?

Why Does the Citadel Explosion Not Appear to Begin in the Sol System?

Take a look at this image showing the location of the initial explosion that is supposed to come from the Crucible/Citadel that then spreads out to all the other mass relays.

There is a rather HUGE problem with this. The Crucible/Citadel is supposed to be in the Sol System/Local Cluster at this point. And this does NOT appear to be anywhere near it.

Let's break this image down to see if we can prove this. First of all let's find identifiable markers to compare to the Galaxy Map.

Here we can see the Nimbus Cluster and a "Y" section that we can identify on the Galaxy map. We can also line everything up using the orientation of the Galaxy core. So lets put a line showing where that is pointed.

OK so now here is the Galaxy map showing these identifying marks plus the location of the Local Cluster, which is clearly nowhere near to the initial explosion.

Here is a composite showing where all the explosions that we see take place.

And this image shows the order in which it takes. Now using what we already figured out, let's overlay this with the Galaxy map and get it to match up with where we know the relays are -

The Local Cluster is not even close to that first explosion! And as you can clearly see the relays match up perfectly, so Bioware knew what they were doing. This is not a case of the animator not bothering the check where the relays were.

So according to our almost undeniable research here, the Crucible/Citadel explosion takes place in the Apien Crest! And the Local Cluster is hit SEVENTH!

How could this have happened? Here are what seem the most likely reasons -

  • The ending originally had the Crucible in the Apien Crest and the animation was done then and never changed.
  • The animator made a huge mistake and paid attention to the relay map but not where the starting position was supposed to be!
  • Bioware intentionally made this wrong along with many other things as a clue that this is not real/true.

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 need 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.

So lets debunk this Catalyst lie to start with. I found this quote from Casey Hudson (executive producer).

Question: So how do you stop something unstoppably massive?

Casey Hudson: That's something we reveal over time. You see humans being harvested and processed to become fuel for the way Reapers reproduce. This is their reproductive cycle and we're just a part of it. We're nothing to them.


So from the mouth of Casey himself, we are NOTHING to the Reapers other than fuel for them to reproduce! They have no interest in "preserving" us to save us from synthetics!

This was from June 2011, so maybe he completely changed his mind as to what drives the Reapers after they were 2 years into making Mass Effect 3. But I doubt it.

Also let's take a look at some of the things Sovereign said to us in Mass Effect 1 -

If Sovereign is not telling the truth about the Reapers contempt for organic life, why? Seems more likely to me that the Reapers see Organic life as something to look down on and use for their own ends, rather than saving us being the sole reason for their existence.

And what species was harvested in the first place to make the Reapers? And harvested by whom if the Reapers were not yet made?

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?

Well Mass Effect 3 lead writer Mac Walters tells us it is only the "Core" of the Reaper that assumes the shape of the original species.

[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 certain 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 their purpose was to preserve all advanced organic races, why did they fail to harvest the Protheans? And why were they building a Human Reaper, not an Asari Reaper since they are the most advanced race.

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. In fact we hear Harbinger dismiss the use of other races for this process in Mass Effect 2 for various reasons, the Asari’s dependence on other species and the Krogan’s genophage affliction.

So it seems logical to presume the Reapers are only interested in using humans to build a new Reaper and wish to wipe out the other species since they are no use and to prevent them warning the future races.

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. And if true, it further illustrates that the Catalyst was lying about the Reapers motivations.


Be sure to let me know what I have missed or if I have gotten any of the facts incorrect. And be sure to read the post EC analysis if for some reason you arrived at this from an older link.


  1. Great collection of evidence. I know it's not 'evidence' per se, but is it worth adding a section about Bioware's history of 'twist endings'? This sort of sets up a 'pattern' of Bioware doing things *like* IT, but not as audacious.

    A list of the games that form this pattern is in the old IT forum on Bioware here:


    I know it is a thin thread, but it does demonstrate prior intent, and that Bioware is certainly 'capable' of this sort of thinking, because they have done it before.

    1. Thanks, this was pointed out to me before but I neve got around to adding it.

      Defiantly worthy of addition, I'll be sure to add it tomorrow.

  2. Dear Parabolee

    Really awesome site you got here, all information in one place, Kudos to that!
    Some Points I wanted to add.
    And please forgive me for posting all this in one comment and not in their respective sections.


    Regarding the counter argument for "The Choices":

    Having destroy as the only option with high EMS doesn't result in resisting

    indoctrination as you won't see the "breath scene".
    You basically need high EMS to be kept alive on earth and pick destroy to resist

    indoctrination through the destroy option, only then you will finally wake up.


    Regarding "Shepard, Anderson and the Illusive Man":

    Maybe you forgot to add that when Shepard shoots at Anderson, you can clearly hear two

    people groan, Anderson and Shepard!
    Possible evidence that Shepard's shot at Anderson actually affected himself/his mind ?


    Regarding "The Plot Holes, strangeness and Illogical Story Elements"

    About the part with Andersons representation of 1000 EMS based on whether TIM shoots him or dies.
    You wrote it was claimed that it depends on whether TIM shoots Anderson or not.
    It's not claimes, it's fact, it's written in the official guide.
    If taken literal, it doesn't make any sense.
    Why is Anderson worth 1000 EMS if he lives a few seconds longer ?
    Whether or not you prevent TIM from shooting him, he dies anyways.
    It's not like he can help you at this point.
    Considering IT though, it actually makes sense bceause, as you already wrote, if Anderson is representing Shepard's remaining free mind, his/it's death would weaken him and make it harder to resist the Indoctrination attempt, therefore higher EMS.

    Maybe you could rewrite that point, because when I read it I found it a bit confusing that you first mentioned it was due TIM's suicide and then added that it's because Andersons's death as an addendum.


    For the "Comments made by Bioware" section:

    In a video interview, Mike Gamble stated that the game would also have the option for a negative ending in which the Reapers would win:
    5:08 mark in the video.

    So if it's neither Control/Synthesis nor Critical Mission Failure, he lied about that as

    well if the current ending is the real one.


    This may due to budget or time constraints, but did you realize that there were a lot of unique-looking Reapers in the ME2 outro (Reaper Fleet) and we saw none of them ?
    See: http://oi50.tinypic.com/2w7on07.jpg

    Also, Harbinger in ME2 and Arrival also had a very different look than in ME3, in which

    he was just reduced to a Sovereign-class Reaper with a missing leg and eyes.
    See: http://oi47.tinypic.com/2wc49vo.jpg

    I don't really understand why, because Harbinger's model was already there, probably just needed some polishing.
    The other ones actually have to be there as well, otherwise they couldn't do the Reaper Fleet video, could they ?


    Hopefully I was able to improve this site a bit :P

    Again, thanks for your effort!

    1. Thanks for your post!

      You mentioned several things I have been meaning to fix and add, thanks.

      The Anderson/TIM one is a result of me changing it to the correct info but not fixing the entire post. I'll do that right away.

      The others are things I have been meaning to add. Thanks to your post I'll remember to do that today :)

  3. Very good work on this blog, one of the most open minded I have found so far.

    There's a few things I'd like to add, the first being my answer to the anti IT question 'if it is about indoctrination, then why give shepard the chance to break free?'

    To answer this I'm going to use a quote from miranda lawson when she explained why the illusive man stopped her from implanting shepard with a control chip.

    'He didn't want to interfere with who you truly were. Something that just obeyed orders, he wanted commander shepard. Installing the chip might have ruined you.'

    This can be apllied to the reapers way of thinking, they want the person who influneced and united an entire galaxy to join their cause.
    They want shepard to come over to their way of thinking and it has to be his/her choice, to deny shepard this choice would be controlling him/her directly and would be no different than an avatar for the reapers will like paul grayson was or simply a husk.
    I believe I can back this theory up with some quotes from saren on virmire.

    'The more control sovereign exherts the less capable the subject becomes, that is my saving grace. Sovereign needs me to find the conduit so my mind is still my own for now.'
    'If I can prove my value I become a resource worth maintaning.'

    Is this logical anaylisis or am I simply grasping at straws?
    This also leads to the question 'if my EMS is low why do I only get one choice?'
    Like you say with high EMS the catalyst says 'Wake up', and when it's low he says 'Why are you here?' This leads me to believe that if your EMS is low the reapers simply don't want you. You're not the powerful leader that they expected and discard you, if your option was to destroy the reapers they kill you, hence the depiction of earth being destroyed, if you option was control you become a mindless tool of the reapers.

    Another thing is a messive hint that I have not seen anyone disscusing on any video or forum, in one of shepard and edi's later they talk about reaper pow camps and prisoner escape atempts and how indoctrination should stop people from helping each other. If you choose the renegade conversation option shepard says 'Maybe the word got out on how indoctrination worked, and they made a decision.' to me this is a massive hint from bioware but I could be wrong.

    Also check out a video on youtube called 'the sounds of possesion', it's about the use of infrasonic sound in the game, does'nt really prove anything but is quite compelling

  4. well , you analyses clues very well .
    i have an other clue: why they bombard the bekenshtine insted of harvest?
    and why catalyst doesnt run Synthesis earlier ? i mean die or Synthesis.
    i will choose Synthesis insted of die .
    thanks for your post . it was nice.

  5. First of all: sorry for my awful English, it's not my first language, so I'll try my best to write as inteligible as I possible...

    I know all the posts are old (and maybe no one will read mine) but wanted to add to Mafrodon quotes one of the conversation with the Catalyst when he explains about the synthesis on the EC, that helps answering this question: "If it is about indoctrination, then why give shepard the chance to break free?'

    Here's the full conversation so you read it in context:

    Catalyst: Add your energy to the Crucible's. THe chain reaction will combine all synthetic and organic life into a new framework. A new...DNA.
    Shepard: Explain how my energy can be added to the Crucible.
    C: Your organic energy, the essence of who and what you are, will be broken down and then dispersed.
    S: To do what, exactly?
    C: The energy of the Crucible, released in this way, will alter the matrix of all organic life in the galaxy. Organics seek perfection through technology. Synthetics seex perfection through understanding. Organics will be perfected by integrating fully with synthetic technology. Synthetics, in turn, will finally have full understanding of organics. It is the ideal solution. Now that we know it is possible, it is inevitable we will reach synthesis.

    And after leading you to think that this is the better solution, that this is what will make everything better, he just says that:

    Shepard: - Why couldn't you do it sooner?
    Catalyst - We have tried... a similar solution in the past. But it has always failed.
    S: Why?
    C: Because the organics were not ready. It is not something that can be... forced. You are ready. And you may choose it.

    "It's not something that can be forced". C'mon Shep, he's saying it to your face.

    It's not that the organics weren't ready, it's just that the Reapers tried to force them and that didn't work, so... what's the solution? Indoctrination. Let organics think that they are choosing by themselves. Let Shepard think that he is choosing by him/herself, and that he is choosing what is right (although he has been fighting against it through 3 looong games and convinced Saren and Illusive Man, and so on, that synthesis is totally wrong and makes no sense). They aren't giving you a chance to break free, they just NEED you to think it is your choice, since forcing you wouldn't work.

    Yeah, I choosed Synthesis the first time I played through and like 30 mins later I started feeling soooooo damn stupid about my choice... It just doesn't make any sense with all the decissions you have made on the whole trilogy.

    1. Good point. I'll be sure to include a mention of this when I finally get around to updating the site for post EC analysis.


  6. Can't see any discusssion over the forth choice? Instead of picking one of the three you can turn around and shoot the kid. This effectively allows the cycle to continue and you get the far future ending that Liara had made plans for?

    1. This was written before the EC. Since then I added this section dedicated to the refuse ending -


  7. About surviving as DNA goo, what are we if not vehicles for the DNA in our cells? It codes our appearances, but more importantly it codes our behavior, our actions, or thoughts, our feelings. What if that is the function of the DNA in the reaper, and it actually thinks and feels like a million humans or any other species they are made of? What if the reapers are indeed an ascended form of those species?

  8. old, but still good. one thing, there's cut dialog between Shepard and Sovereign via the Saren-husk, which has been restored using a mod. Worth checking out.