Harry doesn't see it at first. He doesn't want to see it.
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It's not like there's anything that's really so strange, just a hint here and a clue there, maybe a misplaced word or a cold look. And when he notices that she's starting to walk differently, more confidently, he just figures that she's finally coming into her own. That she's just a late bloomer. He thinks that the -haughty, arrogant- assertive side of her personality is finally coming to the forefront. If it reminds him of someone else, it's just coincidence, right? Flashes of memory –black hair dark eyes red lips- when he sees her are just a fluke.
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When the rumors start reaching him, he starts to wonder. He dismisses them fairly quickly, though. Really, what is the likelihood that Hermione –Hermione, of all people- jinxed Hannah Abbott simply for bumping into her in the hallway? He finds it even harder to believe that she cursed Blaise Zabini for telling a first-year that she was 'that bushy-haired bookworm'. She simply wouldn't do that. And when he asks her about them, she laughs –cackles- and tells him that he's being dense.
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Ron eats it up, of course. He spends nearly every minute spouting on about how he knew she was no good, that any girl who turns him down must have a screw or two loose. After three days, Harry tunes him out. He knows Hermione has her reasons.
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When he catches her practicing curses in the Room of Requirement –real, dangerous curses- he worries that there might be something she's not telling him. The –frightening- determined aura she exudes makes him uncomfortable.He makes an excuse and leaves as quickly as he can, telling himself that he didn't hear the words or see the green flash, that it was just the wind. He ignores the fact that the air he hurries through is as still as the grave. Harry knows that Hermione is a good person, that she has a motive behind everything she does. She'll tell him in time.
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At Christmas, when most of the castle is gone, Harry can't find her anywhere. He knows she stayed behind, so he figures maybe she just wanted some time alone with her books. He resists the temptation to check on her with the Marauder's Map. He knows how important privacy is to her. Later, before the feast begins, he takes a walk around the castle to –find her- clear his mind. He doesn't see her anywhere, but he does hear a couple of third-years giggling happily walking back to Ravenclaw Tower. The sound startles him.
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When she enters the Great Hall, almost half an hour late, Harry is speechless. Not because of her beauty –although he has to admit, she is gorgeous- but because for an instant, he is back in the Ministry screaming for Sirius and fighting the arms that hold him back. He sees sunken eyes and wild hair and a velvety, corset-like dress –but then he blinks, and it's just Hermione, staring at him with a slightly –disdainful- worried look in her eye. It's just Hermione, but the dress remains. Black leather clings tightly to her –oy, look at those- frame, flaring into a deep purple velvet skirt. He suspects that if he could see her feet there would be black boots reaching almost to her knees. She's still staring at him, and he laughs nervously, pretending that the resemblance is just the product of too little sleep. He promises himself a late morning the next day.
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He doesn't believe it, not at first, not even when the proof is staring him in the face. It's almost too much to comprehend, and he takes great satisfaction in not comprehending. He chastises first- and second-years he hears gossiping, and defends her vigorously to older students. He ignores the pitying looks from the Hufflepuffs, the irritated ones from the Ravenclaws, and the flat out entertained ones he gets from the Slytherins. The Gryffindors, though renowned for bravery, aren't quite brave enough to insult Hermione, at least not in front of The Boy Who Lived.
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It's still incomprehensible to him, even when they have to flee from Death Eaters for the third time in a week. Hermione swears that her protective enchantments are working, and Harry doesn't have a reason to not believe her. He tells himself quite sternly that they just have extraordinarily bad luck and will simply have to be more careful in the future. After all, Hermione -kills- jinxes just as many Death Eaters as he does when they make their escapes, if not more. She seems to favor Stunning them to anything, if the amount of unmoving bodies is anything to go by. It's a melee, always, as they flee, and the green flickers he catches from the corner of his eye could have been fired from any one of the Death Eater's wands. Harry tells himself they're unconscious and Apparates away. He can't help but look back, though.
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The first time he hears her leave in the middle of the night, it doesn't bother him. After all, they're wanted fugitives, hiding from capture in a tent in god knows where while their loved ones are in danger. It's enough to make anyone need some fresh air. Harry hears a rustle, then a whisper, then nothing at all. She comes back relatively quickly and goes straight to her bed.
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By the sixth time, he's had enough. She stays out later now, almost two hours the last time, and he was certain that she was leaving the campsite at times. It's not that he suspects her of anything, just that even Ron's started to notice, and if he has to listen to one more inane rant about how she shouldn't be trusted, he might just explode. He pulls her aside and tells her that he thinks it would be best if she stayed in the tent at night. She's reasonable and polite, and somehow manages to get him to agree that since she's perfectly capable of taking care of herself, there's no reason for her to stay inside. Harry walks away feeling shell-shocked, and doesn't –pay attention to- notice the flash of black at the corner of his eye.
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Harry still can't believe it. No, he refuses to believe it, even with her wand at his throat and Voldemort lying with his throat slit in a pool of his own blood behind her. Hermione is his friend, she wouldn't do this! She had her reasons. She killed Voldemort, and that was a good thing, no matter how you look at it. She had her reasons, and she would tell him soon. His train of thought is interrupted by searing, mind-numbing pain. He can barely make out her features. They seem to almost be regretful, like she was watching a movie from her childhood or seeing a book she couldn't afford. She tells him that it really isn't anything personal, that he's in her way and that with him dead, Voldemort will stay dead. She says more, but Harry can't breathe around the silver knife in his chest, and he's more focused on that than anything. Of course, when Bellatrix Lestrange walks in behind Hermione, he tries to snap out of it, to warn her, even to curse her himself. That's why he can't believe it when instead of screaming or running or cursing her or doing anything even remotely sane, she turns around and smiles. Bellatrix grins back –grins, not smirks or sneers or any other expression Harry is accustomed to- and hugs her. Harry is positive that the knife is affecting his brain, that he's beginning to hallucinate in his final moments. Hermione. Is. His. Friend. His vision is beginning to fade, but it's still clear enough to see when Hermione kisses Bellatrix. And when she steps over to his bleeding body on the floor, he still doesn't believe it, even when her mouth moves and green light fills his vision.