Continuing to think about Harry Potter and the Methods of Rationality, the consensus hypothesis seems to be that:
Warning: spoilers follow:
Quirrell is Voldemort. He’s not merely stuck to Quirrell as in canon. He has replaced Quirrell.
Keeping in mind that this is fiction, and that in fiction the author can make the story go anywhere he wants to–Quirrell could be Lion-O of Thundercats if Yudkowsky wants him to be–I think there’s a big problem with this hypothesis. Start with the first postulate of alternative universe fiction: specifically that only a few very carefully controlled changes are made to the canon, and then the story develops from there. In this case the changes are two: Lily Evans uses magic to make Petunia beautiful, and therefore she can marry Michael Verres instead of Vernon Dursley, and Harry grows up in a loving and intellectually curious household. The second change is that Harry is a completely different character who’s way smarter and more mature than the “real” Harry Potter. Indeed you can even argue that this is one change: that Harry’s ridiculous level of intelligence and rationality is a direct result of his different upbringing. (It’s a stretch but you can argue it.) But it stops there. All the other characters are much the same–Dumbledore, Snape, Mcgonagall, Hermione, Ron. etc. They just react to a different set of events.
If this is true, then I think we can rationally conclude that Quirrell is not Voldemort. Of course, if this isn’t true, and if the author is allowing further deus ex machina changes, then the rational plot falls apart.
Why do I think Quirrell is not Voldemort? Simply put: he acts nothing like the Voldemort we know from canon. Voldemort in canon is nasty, brutish, uncaring, violent, and almost completely without self-awareness or potential for growth. He is very much a cartoon supervillain. In fact, now that I think about it I can’t even quite remember exactly what Voldemort wanted to gain by taking over the world. Magical domination of Muggles perhaps? Hitlerian race hatred and genocide? Now that I think about it, it’s a bit of a gap in canon. Indeed Grindelwald (who doesn’t even show up until book 7) has much more fully developed motives. I simply cannot imagine canon Voldemort learning enough to describe his visit to the Muggle Dojo as a failure. Nor is that character subtle enough to maintain the disguise of a Hogwarts professor for months at a time. Quirrell may be an evil character, but if so he is very much a subtle evil character, not the cartoon supervillain that Voldemort is.
We can of course suggest that the character of Voldemort is changed in this story too, much as the character of Harry has. Or we can suggest that even in canon, Voldemort was never more than a puppet of the truly devious HPMOR-Quirrell (not the same person as canon Quirrell), or that Voldemort was just a pretend threat HPMOR-Quirrell concocted out of whole cloth to enable himself to play both sides. It’s fiction, after all, so anything really is possible. But most characters and aspects of the world in HPMOR hew closely to established canon. I find it hard to believe Voldemort is a second exception to the rule.
Update On further research it seems there is little doubt that Quirrell is Voldemort. Indeed Voldemort is a second exception to the rule. In brief, I was working under the assumption that only one change was allowed, but Yudkowsky is allowing more. In particular, “You can’t make Frodo a Jedi unless you give Sauron the Death Star.” In this case, the light saber is that Harry is a lot smarter than in canon, so the death star is that Voldemort is smarter too. What exactly that means I haven’t yet figured out yet, especially as that relates to Quirrellmort’s goals and ambitions. I do think that makes HPMoR a somewhat less interesting story. I think it would have been more satisfying, and allow the same basic story to be told, if Quirrell were Sauron to Voldemort’s Morgoth. This would present a smarter, more devious enemy worthy of the smarter Harry in HPMoR, without twisting canon quite so freely.