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Vanya is a difficult case. But what we're shown makes no actual sense, so here's how we'll manage it:

Vanya never knew that she had powers in the first place. Hargreeves tried to "train" her when she was too young to remember, by herself, because his monocle showed him her great power (which, you would imagine, is how he learned all of their powers since most of them don't physically manifest at random), but it never really worked and it was very dangerous - can you train a baby out of being distressed enough to destroy a room or a house? (Maybe she did kill a nanny, at this point, but it was accidental - she was just a baby, unaware of her powers, only knowing she was starved for attention and affection and upset, and she *cried*.) He started having the nanny put a sedative mixture into Vanya's milk (she was told it was a vitamin supplement to help Vanya grow, as she was very small as a baby). When she was old enough, he switched her to pills that were easier to manage.

The others always thought Vanya was strange and distant from them - after all, Hargreeves was constantly harping on how she was ordinary and useless, she wasn't allowed to train with them or spend much time with them, and she didn't seem to have the same energy or range of emotion they had (due to the sedatives). They didn't outright exclude her - when they had the time to spend together she spent it with them, and they lived in the same house, and all of that - but she felt the distance from them anyway and it hurt her deeply. She felt like the odd one out, and Hargreeves capitalized on that, always quick to remind her that her siblings were special and different and that she was ordinary, useless, worthless, a waste of his money and time.

After Ben died, and one by one the Hargreeves siblings left the home (except for Luther, of course), Vanya did write a book. It wasn't the expose on the lives of the Umbrella Academy children that the show portrays it as, but more of an autobiography about how it felt to live alongside but apart from them while being subjected to Reginald's abuse. Her book did touch on the abuse suffered by the other siblings, which is why they feel offended and upset over it - their trauma wasn't hers to discuss or publicize. Her intentions were good, but she made a mess of the delivery and ended up doing more harm to her siblings, leading them to lose touch over the interim time and to resent her when they meet again as adults.

(She writes the book because she wants the world to know what kind of monster Reginald Hargreeves is, what he did to them. She wants them to stop celebrating him for creating the Umbrella Academy and everything it stands for. She doesn't do it for attention - though she craves it - she does it because she wants to hurt her father. It doesn't work.)

Leonard takes her by surprise. It's not that she's attracted to him, really - she's not attracted to anyone, she never has been, really (thanks, sedatives) - but he listens to her, and he says the right things, and she's touch-starved and he touches her, and he doesn't freak out about how different she is, and he makes her feel like a real human being. He tells her she's extraordinary, and no one has ever told her that before. So she lets herself fall for him, and she gets defensive and upset when Allison tries to poke holes in her relationship with him.

Things fall apart from there. Leonard makes sure she can't take her medication, and Vanya has never had to deal with her actual feelings before. She has no idea how to manage her powers or her emotions whatsoever, and it shouldn't be surprising that everything goes to shit because of it.

(She doesn't lash out at Allison intentionally, or threaten her first. She's upset, angry, and things get out of control. She genuinely can't help it.)

Maybe she can be reasoned with. Maybe she's too caught up in her own anger and fear and guilt that she can't help but want to let that all out - with world-ending consequences. But either way, she's a whole lot less calculated in how she goes about it.