In addition to the rot13'd reason:
It's true in Canon.
Voldemort is the only one with a plausible motive to want Bellatrix Black out of Azkaban.
Quirrel drops a bunch of hints directly:
He says he has resolved his parental issues to his satisfaction, and he says they were killed by Voldemort.
After he got what he needed from the Muggle martial arts dojo, Voldemort comes along and destroys it. Later, when discussing the chamber of secrets with Harry, he mentioned that Voldemort would not leave an important source of power lying around for anybody else to use it, so he probably killed Slytherin's creature.
He tells his whole defense class that he used to want to be a dark Lord.
He tried to become the ruler of magical England by setting himself up as "David Monroe" against Voldemort. Later, once Harry wants to stop being stuck in Hogwarts, he suggests pretending to be Voldemort to set Harry up as a hero everyone else depends on.
He doesn't want Dumbledore to know whom he really is.
At the end of the Azkaban arc, it turns out that is a very large number of identities, so it's not particularly implausible to think that he is Voldemort too.
Also, mysterious feeling of doom. And Quirrel can sense Harry's feelings. And their magic can't interact.
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 96. The previous thread is at almost 300 comments.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system.
Also: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, .
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: