One of the key points of Indoctrination Theory that I think a lot of people misunderstand is it doesn't want or need the endings to change. In fact, it requires everything we've been given up to this point to remain the same. It's an attempt to explain what's going on and what might happen in the future.

In a nutshell Indoctrination Theory says everything we see after Harbinger strikes Shepard down with his beam takes place inside Shepard's mind. Shepard, Anderson and The Illusive Man represent the struggle between Harbinger's indoctrination attempt and Shepard's will to resist it. Starchild and the explanation it gives for the Reaper's purpose is Harbinger's final attempt to get Shepard to willingly, although unknowingly, give in to indoctrination. Everything Starchild says is a lie, the true purpose of the Reapers is still unknown to us.

• Control: You've given in to indoctrination. You've decided The Illusive Man was right. Starchild said The Illusive Man could not have controlled the Reapers because they already controlled him. If Shepard gives in to indoctrination they'll control him as well. Sovereign and/or Harbinger said control is an illusion. This option is colored paragon blue, but it's on the left side, the renegade side, and The Illusive man is shown "taking control". Is The Illusive Man a paragon? It's a trick to get you to think this is a favorable choice.
• Synthesis: You've given in to indoctrination. You've decided Saren was right. Choosing this option means everything you've done since discovering Saren's plans in Mass Effect 1 has been for nothing.

Saren: I'm not doing this for myself. Don't you see, Sovereign will succeed. It is inevitable. My way is the only way any of us will survive. I'm forging an alliance between us and the Reapers, between organics and machines, and in doing so, I will save more lives than have ever existed.

• Destroy: You've resisted indoctrination. Shepard's willpower and resolve overcame Harbinger's attempts and tricks. This option is renegade red, but it's on the right side, the paragon side, and Anderson is shown attacking the conduit. Is Anderson a renegade? It's a trick to get you to think this isn't a favorable choice. This is the only option that allows you to see the N7 breath scene after the credits. Shepard never left London, never used the Citadel beam. After being struck by the beam he resists Harbinger's final indoctrination attempt and wakes up in the rubble after the attack. The fight isn't over. What happens next is to be determined. I think BioWare will release DLC that will allow us to actually finish the fight.

All the post-control/synthesis choice scenes is Harbinger giving you the illusion that your choice was the right one, reassuring you that you did the right thing. The post-destroy scenes is the same thing, reassurance, except that it's Shepard himself thinking it, not Harbinger imposing it on him. None of it is real.

The post-game save is right before the Priority: Horizon mission. Why is that? For one, it says in the mission description that all galactic forces will be committed to the final battle once the mission is started. Having the save at this point allows you the opportunity to increase your readiness rating if you need to before your forces are committed. An effective military strength of 5,000 (I think) is needed to see the N7 breath scene. Two, it gives you the opportunity to make the right choice, to resist indoctrination, and carry on to finish the fight in DLC.

For reference:

Google Doc: A Logical Breakdown of Why the Mass Effect 3 Ending Makes No Sense

Forbes: Did the Real Mass Effect 3 Ending Go Over Everyone's Heads?

There are already roughly 700 threads that discuss the indoctrination theory to one extent or another and your post does not add anything new to the discussion.

http://www.giantbomb.com/mass-effect-3/61-29935/this-video-is-the-best-evidence-for-the-indoctrination-theory-yet/35-540337/#53

oh hey another one of these.

Indoctrination theory is great as a socio/psychological experiment.

Other than that, it is sooooo dumb

@Bane said:

• Control: You've given in to indoctrination. You've decided The Illusive Man was right. Starchild said The Illusive Man could not have controlled the Reapers because they already controlled him. If Shepard gives in to indoctrination they'll control him as well. Sovereign and/or Harbinger said control is an illusion. This option is colored paragon blue, but it's on the left side, the renegade side, and The Illusive man is shown "taking control". Is The Illusive Man a paragon? It's a trick to get you to think this is a favorable choice.
• Synthesis: You've given in to indoctrination. You've decided Saren was right. Choosing this option means everything you've done since discovering Saren's plans in Mass Effect 1 has been for nothing.

Saren: I'm not doing this for myself. Don't you see, Sovereign will succeed. It is inevitable. My way is the only way any of us will survive. I'm forging an alliance between us and the Reapers, between organics and machines, and in doing so, I will save more lives than have ever existed.

• Destroy: You've resisted indoctrination. Shepard's willpower and resolve overcame Harbinger's attempts and tricks. This option is renegade red, but it's on the right side, the paragon side, and Anderson is shown attacking the conduit. Is Anderson a renegade? It's a trick to get you to think this isn't a favorable choice. This is the only option that allows you to see the N7 breath scene after the credits. Shepard never left London, never used the Citadel beam. After being struck by the beam he resists Harbinger's final indoctrination attempt and wakes up in the rubble after the attack. The fight isn't over. What happens next is to be determined. I think BioWare will release DLC that will allow us to actually finish the fight.

All the post-control/synthesis choice scenes is Harbinger giving you the illusion that your choice was the right one, reassuring you that you did the right thing. The post-destroy scenes is the same thing, reassurance, except that it's Shepard himself thinking it, not Harbinger imposing it on him. None of it is real.

The post-game save is right before the Priority: Horizon mission. Why is that? For one, it says in the mission description that all galactic forces will be committed to the final battle once the mission is started. Having the save at this point allows you the opportunity to increase your readiness rating if you need to before your forces are committed. An effective military strength of 5,000 (I think) is needed to see the N7 breath scene. Two, it gives you the opportunity to make the right choice, to resist indoctrination, and carry on to finish the fight in DLC.

Control: colored paragon blue and on the left side because the choice that was associated with the villainous Illusive Man is actually the choice that results in everything surviving (paragon blue) including the Reapers (left side). The Illusive Man is shown just as Anderson is shown for the Destroy ending, showing who's allegiance lies with which choice.

Synthesis: Saren was indoctrinated and wasn't seeking a solution to the Catalysts problem. Saren's alterations were that of the Reapers, the same sort that's present in husks, cannibals, marauders, brutes, banshees, and ravagers.

Destroy: Renegade red and on the right side because this results in the destruction of a all synthetics including the geth and EDI (renegade red) but destroys the Reapers (right side). the only option that doesn't sacrifice Shepards physical form, allowing him to survive the blast on the Citadel he melodramatically decided to walk towards.

>end trilogy

The truth is out there. I want to believe.

@TheHT:

Control: The decision to allow the Reapers to survive is only a paragon choice from the Reapers point of view. They get to survive. It's a trick, you're being manipulated to their way of thinking.

Synthesis: Indeed. We can assume that Saren had no idea of the Crucible or the Catalyst. The thing is - I don't think the Starchild is the Catalyst. I think the Starchild is Harbinger's manifestation of it which it's using to manipulate Shepard. I don't think we know what the Catalyst is yet.

Destroy: The destruction of all synthetics, including the geth and EDI, is a lie. Harbinger is playing on your emotions for your friends and colleagues. It's betting that you wouldn't choose to eradicate an entire race of beings to accomplish your goal. Harbinger is the most dismissive of the destroy choice because it's most definitely the choice it doesn't want you to make.

None of the outcomes, no matter the choice, are literal anyway. The only thing at stake at this point is whether or not Shepard becomes indoctrinated.

@EpicBenjamin: Me too.

@Bane said:

@EpicBenjamin: Me too.

... Anyway, right or wrong, I still think it's cool that people are creating these theories. Just shows how much they care about the universe.

@EpicBenjamin: Ha, I immediately started whistling that tune as soon as I read your comment.

@Bane: I think that the literal ending and the indoctrination theory have about the same amount of plot holes.

I can explain all of the ones from a literal analysis.

There's one you can't explain regarding the indoctrination theory:

Why does EDI disapear when the normandy crash lands on some planete when you choose the ''resist indoctrination'' option

@EpicBenjamin: For the X-FIles tells me so

@Bane said:

@TheHT:

Control: The decision to allow the Reapers to survive is only a paragon choice from the Reapers point of view. They get to survive. It's a trick, you're being manipulated to their way of thinking.

Synthesis: Indeed. We can assume that Saren had no idea of the Crucible or the Catalyst. The thing is - I don't think the Starchild is the Catalyst. I think the Starchild is Harbinger's manifestation of it which it's using to manipulate Shepard. I don't think we know what the Catalyst is yet.

Destroy: The destruction of all synthetics, including the geth and EDI, is a lie. Harbinger is playing on your emotions for your friends and colleagues. It's betting that you wouldn't choose to eradicate an entire race of beings to accomplish your goal. Harbinger is the most dismissive of the destroy choice because it's most definitely the choice it doesn't want you to make.

None of the outcomes, no matter the choice, are literal anyway. The only thing at stake at this point is whether or not Shepard becomes indoctrinated.

@EpicBenjamin: Me too.

Control: It's a paragon choice because the geth and EDI along with any other synthetic survive. It's on the left side, because doing so does not destroy the Reapers or the Catalyst. That's bad because while Shepard has control over the Reapers, theoretically he has the Catalyst to contend with, meaning the Reaper threat could return if Shepard loses or relinquishes control. Or, if the Reapers are capable of modifying themselves to break free from the Catalyst (and Shepards) oversight then they could potentially threaten the galaxy again.

Synthesis: It says it's the Catalyst. As far as we've seen, whenever a Reaper appears in holographic communication, it looks just the same as its actual form, only holographic (we only have the conversation with Sovereign to go on, vs. nothing to support otherwise of course). There's nothing to justify it not being the catalyst. If you think Indoctrination Theory is the support that it's lying, then you're presupposing that you're right, and are making a circular argument.

Destroy: The Catalyst is dismissive because this choice goes undoes its solution (the Reaper harvest cycle) to its purpose (bringing order to the galaxy; preventing synthetics from eliminating all organics) and is also probably dismissive because destroying all synthetics will also result in its own destruction.

@pyrodactyl: If you can pull some points from the video or Google doc and explain them from the perspective that the choices and endings are literal that would awesome. I think the only thing literal about the ending is BioWare literally ran out of time to complete it.

I'm not sure why you think EDI disappears from the Normandy if you choose destroy. You're the first to suggest that that I've seen.