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Nightmare Fuel: Kare Kano
Spoilers below:
Arima's dark side. Any time that he comes onto the screen, you just know Arima is seconds away from shattering. This is made worse because to the outside world, he appears to be a put together, genius with his only match being Yukino, his girlfriend. It's scary to slowly see his thoughts morph from wanting to be with Yukino, to wanting to isolate her from everyone and keep her just for himself. His fighting with these thoughts proves that Arima is a good guy, but him imagining tying Yukino in chains does not bode well for their relationship. This is a rare case of Stalker with a Crush in which not only is the stalker in a committed relationship with his crush, but he is also portrayed as so sympathetic that you just want to save him from himself.
The worst has to be the end of Chapter 42 right after Yukino decides that she wants her world to be bigger than just her and Arima. The realization that he cannot bind her to him makes the dark side that Arima was always trying to hide come out. And it is frightening.
He also stabs himself in the freaking hand in Chapter 72, after he accidentally rapes her, in order to atone for his mistake.
Yukino's last-ditch attempt to save him can also qualify actually arguing with Arima about whether or not he raped her (he believed he did but she insists otherwise) and then she smashes her hand on glass to mirror his own hand injury.
Before all that, Ryouko's treatment of child!Arima. It's both horrifying and tear-jerking to the nth degree. It can be considered Nightmare Fuel because he could have almost frozen to death had his adopted parents not rescued him.
Even more so. He wouldn't have necessarily frozen to death... he would've likely bled to death, since Ryoko had beaten him severely beforehand.
And seeing Soichiro's broken little body in the snow from Reiji's perspective was pretty horrifying too.
His father Reiji's childhoold wasn't much better. His mother went insane and tried to drown them both. The only reason Reiji survived is that he kicked her in the face until she let go.