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* Quirrell seems to be taking his teaching duties seriously, marking boring homework assignments and [[spoiler:advising Hermione to leave Hogwarts for her own safety (though there might be other motives for that)]]. This seems at odds with his cynical, unconcerned attitude, until you realise [[spoiler:there was a time in canon that Voldemort wanted to be a Defence Professor.]]
* Moody thinks rather than using a trapped Triwizard Trophy to teleport a victim (with a completely pointless return charm on it), an intelligent dark wizard would have someone simply toss the target a trapped Knut on their next visit to town. Quirrel used this exact method to take Harry to Diagon Alley (albeit consensually) earlier in the story, making this a call back (and reminder of Methods!Quirrel's [[GenreSavvy genre-saviness]] compared to canon Voldemort).
* In Chapter 74, the students who encourage Pansy Parkinson to think her soul has been eaten are all members of the Chaos Legion.
* Quirrel's [[RefugeInAudacity answer to Dumbledore]] after [[spoiler:Harry killed a dementor]] makes us wonder why nobody caused him any problems after a SarcasticConfession of this sort. Until we realize that the only people who would take this answer at its face value are those who know the answer to the "[[spoiler:What lies at the center of a Dementor?]]" riddle, and those who had weren't likely to find Quirrel's goal in life to be all that bad.
* On the same note, what everyone [[spoiler:except Harry]] hears the Dementor say to Professor Quirrell is that "it knew [him], and that it would hunt [him] down someday, wherever [he] tried to hide." Harry assumes this is just something they've all constructed, rather than something the Dementor has actually said; whether or not this is true, the reader knows there's more meaning to that threat than the characters assume.
* In Chapter 89, all the chracters who try to stop Harry are from the Chaos Legion, and those who help him are from the Sunshine Regiment
* Daphne's [[spoiler:lightsaber]] is a [[spoiler:Blade of Greengrass]]
* Dumbledore's "there would be nothing left of the world but fire!" in chapter 61 is what Severus is thinking of when [[spoiler:Rianne]] says "they would catch fire and burn the cauldron" in chapter 76.
* The Interdict is a very good reason to make people immortal.
* In chapter 74, Quirrell describes an old and terrible ritual, one intended to summon up Death - involving a noose that has hanged a man, and a blade used to kill a woman. He mentions offhandedly that the ritual to counter this has been lost to time. This sounds ''remarkably'' like the cause of the Dementors...
* Crosses with FridgeHorror, in Chapter 103, Quirrel gives [[spoiler:Hermione a D on a Ministry exam, and laments that he would have given her a lower grade, but that would have been "in poor taste".]] Considering how, in canon, the only [[spoiler: grade lower than a D is a T... for ''troll''...]]
* Harry worries that the Line will be intercepted by a subtly evil heir, but this will not happen if Harry himself succeeds in living forever, or hands it to Hermione when he fails to as she is almost guaranteed to live forever. Unless this is the one where [[FridgeHorror Harry himself turns evil]], in which case everyone is screwed.
* Minerva's presence ''did'' make a final difference to how the [[spoiler:prophecy]] turned out. If it had been just Severus there with Trelawney, obviously he would have figured out that it was meant for him, and that would have required it to be even more ambiguous and subtle to make him still go to the Dark Lord with it before working out what it meant.
* Chapter 109: when Voldemort regains his faculties the mirror summons Dumbledore. Why? Because Voldemort's deepest desire is for a worthy opponent.
* At the end, when Voldemort summons the Death Eaters, he doesn't call them by their proper names - rather, Mr. White, Mr. Grim, et cetera. This is a very definite CallBack to [[http://hpmor.com/chapter/7 chapter 7]] where Harry requests that Ron call him 'Mr. Spoo', and they eventually settle on 'Mr. Bronze'.
* [[spoiler:Sirius]] is called Mr Grim because he can (or could in canon) [[spoiler:turn into a big dog that looks like the omen called "the Grim"]] in Divination.
* If horcruxes work the same way as in canon, then [[spoiler:someone has been horribly murdered while in the presence of the Pioneer plaque]] and the deed has been covered up afterwards.
* When Draco is briefly [[spoiler:forced to consider siding with Dumbledore]], he decides he'd rather be burned alive. And then when you read it again with the knowledge that Draco believes [[spoiler:Dumbledore killed his mother by burning her alive while she slept]], that comparison becomes rather [[TearJerker horrifying]]. And very similar to the decision that the Potters took -- dying rather than letting Voldemort kill Harry.
* The story indicates that teachers can freely use memory charms on students without oversight or appeal (after the ritual incident, Snape modifies over a dozen students' memories without the Headmaster's knowledge). While we haven't seen any actual abuses of this, there have been tales of Defence professors who really get around or are more ObviouslyEvil than Quirrel, and if, like Snape, they can do it without Dumbledore's knowledge, the implications are not pleasant.
* If Harry's theory about how Fred and George pranked Rita Skeeter is correct, then Fred and George were able to [[spoiler:False Memory Charm her and get away with it.]] The scale of the pranks they (or less honorable people) could effect with that method are frightening. Which, in hindsight, actually makes it a bit heartwarming that they erased the knowledge of how they did it.
* When Hermione calls Quirrell evil: ''"Miss Granger," Professor Quirrell said gravely, "it can be dangerous to give people compliments like that when they have not been truly earned. The recipient might feel bashful and undeserving and want to do something worthy of your praise...."'' And what happens in the next arc? [[spoiler:Hermione dies horribly.]] Coincidence?
* If TheReveal in chapter 102 of the [[spoiler: true functionality of the Horcrux spell]] [[UnreliableNarrator is true]], and [[spoiler: the Pioneer Plaque is indeed a Horcrux]] then Voldemort has successfully [[spoiler: ''fucked'' the Plaque's message of peace]] and [[spoiler: introduced ''all of humanity'' as ''assholes'' to any aliens who find it, as whichever alien picks it up will get MindRaped. NiceJobBreakingItHero]].
* [[spoiler:Bellatrix]] got splinched. Evidence: her severed arm still moves, and her Dark Mark was still active enough to be used to call others. She was probably off somewhere feeling still connected to it, blood flowing from her body to it and back. Imagine how she must have felt when it got [[spoiler:incinerated]].
* The extent of how dangerous magic can become, as mentioned in chapter 119. Attempts on the quantify the risk of just transmutation on forums or reddit have ranged from the civilization-ending (a few nuclear weapons or biological weapons) to the world-ending (a black hole) to tearing apart stars within several hundred light-years (transmuting an ultra-dense volume of charged subatomic particles like packed electrons) to universe-destroying (violating colour symmetry by transfiguring a single red quark, transfiguring up a lower vacuum state). Given that this same society considers locally suspending the Newtownian laws as an afternoon's work, or what the hidden law of potion making might mean to someone who really understands what makes up iron or uranium, it's quite probable someone might mess around with these aspects by accident even before working with transfiguration.
--> ''All it might take was one single Muggleborn who knew the names of the six quarks deciding to try it. That could be the clock ticking down to the prophesied end of the world.''
On the [[Headscratchers/HarryPotterAndTheMethodsOfRationality headscratchers]] page.