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Tearjerker: Harry Potter and the Methods of Rationality
Chapter 39, during a heated discussion, when Dumbledore tries to explain to Harry that there is evidence of afterlife.
Harry: All right, I'll hear out your evidence, because that's what a scientist does. But first, Headmaster, let me tell you a little story. You know, when I got here, when I got off the train from King's Cross, I don't mean yesterday but back in September, when I got off the train then, Headmaster, I'd never seen a ghost. I wasn't expecting ghosts. So when I saw them, Headmaster, I did something really dumb. I jumped to conclusions. I, I thought there was an afterlife, I thought no one had ever really died, I thought that everyone the human species had ever lost was really fine after all, I thought that wizards could talk to people who'd passed on, that it just took the right spell to summon them, that wizards could do that, I thought I could meet my parents who died for me, and tell them that I'd heard about their sacrifice and that I'd begun to call them my mother and father — Dumbledore: Harry — Harry:(furious) And then, I asked Hermione and she said that they were just afterimages, burned into the stone of the castle by the death of a wizard, like the silhouettes left on the walls of Hiroshima. And I should have known! I should have known without even having to ask! I shouldn't have believed it even for all of thirty seconds! Because if people had souls there wouldn't be any such thing as brain damage, if your soul could go on speaking after your whole brain was gone, how could damage to the left cerebral hemisphere take away your ability to talk? And Professor Mc Gonagall, when she told me about how my parents had died, she didn't act like they'd just gone away on a long trip to another country, like they'd emigrated to Australia back in the days of sailing ships, which is the way people would act if they actually knew that death was just going somewhere else, if they had hard evidence for an afterlife, instead of making stuff up to console themselves, it would change everything, it wouldn't matter that everyone had lost someone in the war, it would be a little sad but not horrible! And I'd already seen that people in the wizarding world didn't act like that! So I should have known better! And that was when I knew that my parents were really dead and gone forever and ever, that there wasn't anything left of them, that I'd never get a chance to meet them and, and, and the other children thought I was crying because I was scared of ghosts — The old wizard's face was horrified, he opened his mouth to speak — Harry: So tell me, Headmaster! Tell me about the evidence! But don't you dare exaggerate a single tiny bit of it, because if you give me false hope again, and I find out later that you lied or stretched things just a little, I won't ever forgive you for it! What's the Veil?
Also and more so the very next chapter, Chapter 47.
Bellatrix's hands were still chained to the broomstick, so it was only a finger that came up and pointed when she said, "What is that?"
Harry followed the direction of her finger and saw... nothing in particular, actually...
Then Harry realized. After they'd gone up high enough, there hadn't been any clouds to obscure it any more.
"That is the Sun, dear Bella."
"You went to Azkaban," Harry whispered, "you took Fawkes with you, he saw - you saw - you were there, you saw - WHY DIDN'T YOU DO ANYTHING? WHY DIDN'T YOU LET THEM OUT?"
Sometimes you call your brain and it doesn't answer.
Every description of Hermione during chapters 80 and 81. Reminding you personally that this is an 12-year-old girl that thinks she is about to be thrown to the Dementors. (AND has been magically convinced that she's guilty to boot!)
While unlikely and even if true her responsibility was greatly diminished, it's possible that she is guilty: the pureblood faction would respond unpleasantly if the Blood-freezing Curse that she was alleged to have used were beyond the abilities of a merely better-than-average first year student, or were not cast by her wand (the ability to check what spells were most recently cast from a wand showed up very early in the fic). She'd been False Memory Charmed into believing that Malfoy was planning to do something ultimately terrible, but neither the government of the UK nor the US recognizes a legal ability to kill to prevent another citizen from enacting vague and far-off harmful acts: self-defense or defense-of-others requires immediacy that Malfoy would not have presented, since he wanted to challenge her again in the next morning. In short, she might well have been memory charmed (or Obliviated and then fed false information based on a previous save scum) in such a way as to believe that outright murder of someone who had just recently helped her was not only acceptable, but mandatory. The same girl that just a few chapters before could tell Light and Dark in a simple bright line. In a work by a writer who is very, very certain as to his opinions on the death penalty. So, how about that High Octane Nightmare Fuel and Tear Jerker combo?
Don't forget chapter 84,
It should have meant something to her, should have touched her. Should have made her felt better inside, that Dumbledore, who had seemed so reluctant before, had now acknowledged her as a hero.
She felt nothing.
Hermione let her head fall back to the bed, as Madam Pomfrey came and made her drink something that seared her lips like the afterburn of spicy food, and smelled even hotter, and didn't taste like anything at all. It meant nothing to her. She went on staring up at the distant stone tiles of the ceiling.
Hermione suddenly convulsed, her arms twitching into the air as though reaching up for something, and her eyes flew open again. There was a burst of something that was magic and also more, a shout louder than an earthquake and containing a thousand books, a thousand libraries, all spoken in a single cry that was Hermione; too vast to be understood, except that Harry suddenly knew that Hermione had whited out the pain, and was glad not to be dying alone. For a moment it seemed like the outpouring of magic might hold, take root in the castle's stone; but then the outpouring ended and the magic faded, her body stopped moving and all motion halted as Hermione Jean Granger ceased to exist.
Professor Mcgonagall's speech to the Hogwarts students after Hermione's death and right after when she goes to Harry.
Harry stared at her, then made a odd noise that sounded like it had been forced from his throat, and covered his face in his hands. So she knelt down, and hugged him. It might go wrong, but it might also go right, and she would not let that uncertainty stop her; it was time she began to learn a Gryﬃndor’s courage, so that she could teach it in turn. “I had a sister once,” she whispered. Just that, and nothing more.
Neville after Hermione dies and Harry moves to send him away from Hogwarts since it isn't safe:
"I don't want to say goodbye," Neville said. His voice was trembling, but he managed not to cry. "I want to stay here and fight with you against - against whatever's happening."
The empty air moved closer to him, and embraced him in a hug, and Harry Potter's voice whispered, "Tough luck."