That’s right, you don’t. Granted, a lot of IT supporters don't understand it either (even Byne). Specifically, what IT is about. Or rather, what it should be about. Literalists and theorists alike pay attention. Let me try to break it down for you.
WHAT INDOCTRINATION THEORY IS ABOUT
IT at its core isn't about the dream sequence, or hallucinations, though we do deduce them. IT isn't about trivializing the ending or retconning it, quite the opposite in fact. IT isn't about hoping Bioware will come up with a better ending down the line, since we hope not for new endings but new epilogue material. And IT isn’t about disrespecting Bioware or its writing talents. In fact we’re celebrating it.
IT accepts the ending we saw as the ending we have. IT accepts that the ending we saw is the culmination of the series. IT accepts that any DLC related to the ending or post-ending will not change the fundamentals of ME3’s ending.
What IT is actually about is this: The primary plot of ME3 is not just saving the galaxy from cuttlefish. It’s the struggle for the soul of the galaxy against hostile powers that would devour it. Shepard’s journey is central to that, and decides the outcome. You must overcome deception, manipulation and temptation to achieve victory. If you fail, if you let fear or doubt compromise your judgment, you will become a tyrant just like the monsters you fought.
The entire series has revolved around ethics, their diversity and the conflicts that arise from them. It establishes the setting, defines characters, and is the focus of virtually every important mission in all three games. The reapers and their indoctrinate agents are antagonists because above all else they are unethical, and they drag all other life around them down to their level, where terror and suffering are deemed acceptable and where compassion cannot be found.
According to IT, if you choose either Control or Synthesis, you were brought down to that level. To some degree you will have accepted the reapers’ justifications for the unjustifiable. You will have believed the unbelievable. You will have trusted the untrustworthy. You will have betrayed everything and everyone you fought for throughout three games, and you will have done so for dubious promises or empty self-satisfaction. You will have robbed the galaxy of the chance to build a future for itself because you accepted a future that your enemy presented to you.
But if you choose Destroy or Reject*, you will have beaten their efforts to turn you. You will have accepted the terrible price, real or imagined, but saved the integrity of galactic life. You will not have compromised with the planet raping cuttlefish who spread terror and madness wherever they tread. You will have had the good grace to know right from wrong, no matter what code of ethics you stand by.
Basically, you must choose Right against immense encouragement to choose Wrong. That’s the fundamental idea of Indoctrination Theory.
It’s not that the ending is a dream or there’s a reset button. We think there was a dream, but that doesn’t mean what we saw didn’t matter, and it’s not a necessary component to the core idea. Hell, you can imagine the end sequence as actually happening completely and this idea can still be valid. And the EC did nothing to dispel it as invalid. But of course the theory is not just this idea but involves larger case surrounding it…
*We can’t agree on whether or not Reject is in fact a victory condition. There is simply too little information regarding it to agree one way or the other.
THE CASE FOR INDOCTRINATION THEORY
The Catalyst appears as the Earthchild. Thus we can conclude that the Catalyst was actively directing Shepard’s perceptions. Since it openly associates with the reapers, encourages choices reminiscent of the goals of indoctrinated villains, and provides no proof but its word that it is not the enemy still, we conclude that the Catalyst is trying to manipulate us for its own ends and not Shepard’s benefit. From here we can begin to build a case for an indoctrination attempt occurring in the final minutes of ME3.
We see Shepard waking up in rubble that is one iota shy of being undoubtedly London rubble, thus we conclude dreams and hallucinations. Granted we can’t determine exactly what the balance is between reality and fantasy between different shots let alone different scenes. But dreams have already been used in the series before both as plot vehicles and as established vectors of indoctrination. From this we can establish method.
We find that Shepard has canonically been in the vicinity of indoctrinating presences for significant periods of time (not even getting into optional opportunities such as Arrival), and that Shepard does exhibit established symptoms of undergoing an indoctrination process. Coupled with the absence of reason to believe otherwise we conclude that Shepard must have been touched by indoctrination to some degree by the time of Priority: Earth. We can establish opportunity.
We see the reapers behaving completely contrary to what should be expected, including allowing the relay network to remain functional and Harbinger implausibly failing to kill Shepard. From that we conclude that the reapers were planning to indoctrinate Shepard for their ends. Considering Shepard’s achievements and significance, and therefore Shepards possible usefulness to the reapers as an indoctrinated agent, we can establish motive.
Method. Opportunity. Motive. We have a case for Shepard undergoing indoctrination. It’s a solid case. It’s a mother beautiful case. It’s coherent and consistent with the rest of the series. It’s based on facts. It answers so many questions and fixes so many problems. There are literally hundreds of pages of circumstantial evidence in support of it…
SO WHAT’S THE PROBLEM
The case is plausible. But it’s a Watsonian case, not a Doylist one. This is where I think most of the problems and schisms in the fanbase regarding IT come from.
Many theorists leap to the conclusion that the Indoctrination Theory must have been consciously implemented by Bioware. But that’s a separate theory entirely. It’s its own case that must be evaluated as such. And it’s a much trickier case. Whilst Bioware certainly had the method and opportunity to implement IT, the arguments for their motive to do so still are still shaky, many of the implications if the case turns out correct can be construed as unpleasant, and there is simply not a strong body of evidence, circumstantial or direct to support it. There is the curious presentation Earthchild’s introduction, and there is Shepard spontaneously developing TIM eyes in Control and Synthesis, there’s even Coats’ odd cameo in the Citadel corpse pile, but there is honestly very little else that approaches anywhere near solid that Bioware intended IT.
You can’t use the majority of the body of circumstantial evidence for Indoctrination Theory to support “Bioware Intends IT Theory” because that’s trying to apply Watsonian evidence to a Doylist argument. Many literalists here have done the exact opposite. They bring up evidence that could be construed as “bad writing”, whether it be inept, lazy, ham-fisted, etc. to discredit IT. But that’s trying to counter a Watsonian theory with Doylist arguments.
Either way, it’s essentially comparing apples to oranges. You can argue the merits of Indoctrination Theory with Watsonian evidence. You can argue the idea that Bioware intends IT with Doylist evidence. But please for the love of all that’s good on this planet stop being dolts and mixing them up. They’re separate theories that need to be evaluated and dealt with separately. And stop falling for your confirmation biases. It’s lazy and stupid. It’s bad speculation.
I like Indoctrination Theory. It’s my head canon. But I’m currently completely agnostic about believing whether Bioware will actually embrace it as canon or not. I usually lean against the idea. What I know is that IT is for the moment only a theory. It’s a plausible, valid theory, but it’s not a proven fact. And the only trier of fact who can confirm or debunk it as fact is Bioware.
But then again it shouldn’t be disparaged because it’s only “wishful thinking”. Indoctrination Theory is about choosing Right from Wrong. Its purpose is to provide closure. It provides coherency and depth to what is otherwise a shallow and broken conclusion. If you disagree with these statements, either provide good alternatives or get the hell out.
TLDR: F*ck it, just read the damn wall.

- Simon_Says