The Catalyst, appearing at the end of Mass Effect 3, appears to be an instance of a classic trope for the final challenge a hero must confront: the Devil, more specifically in the sense of Satan, who is ambiguously either God's enemy or God's prosecuting attorney. To be clear, I don't mean this is actually intended as a religious message; I'm just trying to describe the nature of the trope. That is, the Catalyst is an immensely powerful and intelligent being, who cannot simply be defeated through cleverness or martial skill; the Catalyst is a moral challenge, and the form of this challenge is a familiar one, with familiar rules: the Devil will offer you a choice. The apparent reasoning behind the choices will be strong, and usually the Devil only lies by omission, but all choices are damning, and all must be rejected; only then will the real answer become apparent. The most important part of the challenge is that the hero must refuse all the options, despite the apparent absence of any alternatives. That's a familiar trope to many people, and the form of it is similar to many of the choices Shepard has already had to make: for instance, when Shepard was asked to choose between the Quarians and the Geth at Rannoch, Shepard had the option to insist that, "No one else needs to die today", and broker an immediate peace. So many people describe reaching this final decision, and being puzzled: the rules of the trope were broken. There was no option to reject the choices offered. There are variations on this trope, and I think there's some ambiguity about which variation ought to apply; perhaps the writers wrote themselves into a corner here. In one variation, the Devil represents something utterly beyond what the hero can overcome. The only thing the hero can do is refuse the choice offered by the Devil and hope for rescue by something even more powerful than the Devil. Early in Mass Effect 1, it looked like the Protheans might represent something more powerful than the Reapers, but it soon became clear that they were just another galactic civilization that the Reapers destroyed, who weren't actually more powerful than current civilizations. That the Reapers, and the Catalyst, would represent a challenge of this magnitude, fits with the idea of "cosmicism" that has been suggested as part of the setting: that there is an ultimate logic to the universe, but it is beyond human comprehension. The problem, of course, is that without any sign of anything more powerful than the Reapers, there is no alternative to the choices offered by the Devil. This means that the hero is completely defeated. The other variation is that the Devil isn't actually as powerful as it looks; it has a hidden weakness, or there is a critical flaw in its reasoning, which allows the hero to finally outmaneuver it and triumph. Classic example (though the heroic decision was made very early in the narrative): the One Ring apparently offered the choice of using it to defeat Sauron, or surrendering to Sauron; instead, Gandalf proposed destroying the One Ring, which Sauron didn't expect. In ME 3, it appeared to be more straightforward: for the first time in millions of years, most or all of the civilizations of the galaxy are united in opposition to the Reapers, and they have finally constructed the Crucible, but don't know how to trigger it. So I think most people expected Shepard to be able to tell the Catalyst to take his choices and stuff them, then for Shepard to press the big "I Win" button. From that perspective, the Indoctrination Theory seems to fit a lot of the expectations, but with two obvious problems: there is no explicit rejection of the choices offered by the Catalyst, as Destruction was one of the choices offered; and there is no clear confirmation that Shepard has made the right choice. There's also the bit about the destruction of all synthetic life, i.e., EDI and the Geth, but that could be dismissed as a lie. Like a lot of people, I find that the Indoctrination Theory has a strong appeal, but I can't quite convince myself that it's actually intended -- the way it is chosen doesn't quite fit the trope of rejecting the choices offered by the Devil, and there's no definite confirmation that one has made the right choice. I'm more inclined to conclude that the writers wrote themselves into a corner, in which they felt the Reapers had to be beyond the protagonists, but they could not introduce a greater force that could overcome the Reapers.