Here's mine:
cold!Harry activates his Patronus charm, which depends on the wish to destroy Death, and therefore can be cast while "cold". This is done to disrupt the proceedings by destroying the Dementor. Since Harry never actually did this while at Azkaban, he wouldn't necessarily be associated w/ the prisonbreak of Bellatrix.
In the confusion, Harry cloaks himself, and timeturns back an hour. This is done to give himself time to contemplate exactly what he needs to say and do. Sicne he will be cloaked, this preserves the secret of the Time turner.
(version A) Immediately after destroying the Dementor, and the loop is closed, still-cloaked Harry takes advantage of his ability to get past any guards/defenses and whispers in Parseltongue into LM's ears: "No power can stop me. Even here in the Wizengamot I could reach you. If you do not relinquish your claim on Hermione your son is dead." IF LM doesn't understand Parseltongue, he would at least recognize it, and Harry could repeat himself in English.
Harry Time turns again, and uncloaks in a side hall, intentionally getting himself seen during the same time that cloaked!Harry was threatening Draco's life (the sole real leverage over LM Harry has.)
This is the scenario I view being conducted.
3 (version B): instead of repeating his words in English, he could leave the his mother's potions book at LM's feet, with a note in English that says the same... with the added phrase, "Contained within this manual is the key to a terrible secret that would destroy Dumbledore. You have gained, this day, Lucius Malfoy. I have uses for the Granger child yet. Do not interfere in my plans." This has the added benefit of ensuring that LM is likely to stay quiet about the threat -- because the pot was sweetened in favor of blackmail of Dumbledore by Lucius.
Since Harry never actually did this while at Azkaban, he wouldn't necessarily be associated w/ the prisonbreak of Bellatrix.
But Dumbledore's Patronus can identify Harry's Patronus, and so Dumbledore could find out that Harry was in Azkaban when Bella was broken out.
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
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: one, two, three, four, five, six, seven, eight, nine, ten.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
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: