Voldemort had the ability fly free from his body.

At least, Harry thinks that he did. (The last sentence I quoted is the section that I had misinterpreted as evidence that he couldn't, but I wouldn't take Harry's speculations as the most likely possibility instead of a conservative estimate.)

On /r/HPMOR, some have been speculating that Dumbledore coated the Philosopher's Stone with Bahl's Stupefaction, which you might remember from chapter 63:

"Bahl's Stupefaction," Moody said, naming an extremely addictive narcotic with interesting side effects on people with Slytherin tendencies; Moody had once seen an addicted Dark Wizard go to ridiculous lengths to get a victim to lay hands on a certain exact portkey, instead of just having someone toss the target a trapped Knut on their next visit to town; and after going to all that work, the addict had gone to the further effort to lay a second Portus, on the same portkey, which had, on a second touch, transported the victim back to safety. To this day, even taking the drug into account, Moody could not imagine what could have possibly been going through the man's mind at the time he had cast the second Portus.

This would explain why Voldemort let Harry keep his wand after swearing the Unbreakable Vow, and now also might explain Harry's recent actions.

I was wondering if one of the things Harry would do with his extra hour was a Patronused message to Lucius to "Stay where you are, remain silent, do not respond to the Dark Mark, for one hour, if you want to live." Or even better, a message to Draco to send that message to Lucius, except Draco is probably still sleeping off Harry's stunner.

In any case, under the circumstances, Harry might be able to trade the whole sad story, including confirmation of Dumbledore's ordered killing of Narcissa (now that Dumbledore is gone) for Draco's forgiveness.

Didn't Harry JUST learn a lesson about not keeping secrets and assuming he's smarter than the rest of the world put together?

Would you risk going back to a live LV just to check it out? Take the risk that Harry didn't notice some annoying bystander get dispatched, or just didn't mention it? A lot of those revelations only came out when the subject came up, after all. Using a Pensieve would be much safer.

You assume Snape isn't one of the headless minions on the ground...

I'm with everyone else on the wand thing. It would have been simple enough to have him drop it. One narrative explanation for getting the wand back into Harry's hand would have been V asking for a demonstration of PT after Harry told him of it. Another would be to throw away the simplest timeline thing and let time-turned Harry come to the rescue with that solution, wand, cloak, etc. in hand. Though I don't know why V left him an hour on the time-turner either.

But:

My real confusion starts way before all of this. You have the idiot-child of prophesied destruction, and what you do not do is back him into a corner where he may decide to do something desperate. Making Harry feel threatened was a big risk to take with that prophecy.

V transforms into a super scary villain, putting Harry under massive duress, the exact kind of thing that would possibly cause him to destroy the world through time paradox or some other unknown power. It would have made more sense to bind him with an unbreakable vow long before then, to maintain the pretense of friendship throughout. So he guessed you're Voldemort, fine. Come clean, acknowledge what your plan to rule Britain was, and that you have been planning to place Harry as the ruler this time. Have that discussion. Come clean about the existence of a prophecy. Tell him you intend to resurrect Hermione. That you need to know what secret power he has so you can help him avoid the inadvertent destruction of the entire universe. Remind him of the centaur prophecy. Get him on your side that he is a serious risk to everyone. Brief the Death Eaters ahead of time, have a few that Harry doesn't know present out of uniform for a fake ritual of divination that supposedly requires him to be completely nude and holding no objects. At the agreed upon time in the ritual they all just AK him and Harry dies with his eyes wide going "Wait, WHAT?" and thinking you were his friend until the last.

V broadcasts his betrayal so far in advance, and that seems downright unsafe given what is at stake and what a giant question mark this boy is. You underestimate a 1st year, sure. But you don't underestimate a 1st year who is prophesied to destroy the stars and you, who you know has unknown powers.

I'm not hating though, EY. You're writing the story, not me. I know it's taken a lot of effort and I've enjoyed it immensely and I thank you for taking all of this time to write what has essentially been a free novel for all of us to consume and form a community around. I don't usually even think that hard about the fiction I read, but your story invites me to do so. It's been a great experience and I look forward to the finish.

Let me have a go at coming up with a dozen:

• Get rid of Harry's wand (as mentioned)
• Remove Harry's glasses (which could have been a transfigured anything, and Voldemort had just taught Harry how to dispel transfiguration by mere physical contact)
• Bind or paralyse Harry, with rope or a Death Eater spell
• Have a Death Eater Imperius Harry with a command to obey Voldemort and do nothing else
• Have a Death Eater use a Confundus Charm on Harry to make him trust Voldemort and not look for ways to escape
• Blind Harry - he doesn't need his eyes to tell Voldemort his secrets, just his ears and tongue
• On the same principle, Voldemort could happily dismember him, as long as magic was used to prevent death from blood loss or shock, and distraction from pain
• Drain Harry of magic by forcing him to cast innocuous spells
• Use illusions to disguise the number and location of the Death Eaters so that Harry is unable to come up with targeted countermeasures against them (and so are any unexpected rescuers)
• Cast a spell on Hermione as a dead man's switch - something that will not permanently hurt/kill her unless Harry does something to incapacitate Voldemort and prevent him from dispelling it in time (not violating Voldemort's promise, since he does not expect Harry to do this)
• Have one of Voldemort's innumerable horcruxes and a tied-up victim on hand so that he can come back immediately if killed (if there's a mandatory time delay, Harry doesn't know it, so this is at least a powerful bluff)
• Bring in some hostages, and kill one each time Harry starts doing anything that sounds like playing for time rather than being maximally cooperative

That took me about 15-20 minutes.

Something that could indicate trying to dodge, or consciousness leaving the body. It's not unreasonable for Voldie to think "I've lost here, no matter what I do this body will be unusable in the near future, in case he has a plan to incapacitate me without triggering my Horcrux wards I'd better go someplace else".

It is implied that while Voldemort can stop possessing a victim at will, he cannot stop inhabiting his own body at will.

[EDIT]Though Harry internally states the opposite:

He cannot be imprisoned, for he can abandon his body at any time.

This is the part I was thinking of:

The soul he'd created for himself had to be anchored in this brain, it mustn't be allowed to float free.

So... Quirrel told McGonagal that he was David Munroe, and it was implied with Madam Bones. It looks like David Munroe was killed in a battle with Voldemort, ending that noble and most ancient line, which has now been avenged by Hermione destroying Voldemort with her magic Girl-Who-Lived powers.

Are we going to get the Noble House of Granger? Does the House of Potter lose its noble status since David Munroe was apparently not previously dead to be avenged by Harry? Will they both be noble because the Wizengamot doesn't know what to do with the ambiguity?