One possible reason could be that Hermione realizes she has feelings for Ron and wants to avoid any confusion or mixed signals with Harry. She might think that by pushing Harry away, she can focus on her true feelings for Ron.
It could be that Hermione has a grand plan in mind that she can't share with Harry at the moment. To ensure the plan's success, she needs to distance herself from him. Maybe it has something to do with fighting Voldemort or protecting Hogwarts. She might believe that by pushing Harry away, she can better execute her plan without his interference or concern for her well - being.
One possible reason could be that she was in love with someone else and couldn't resist the temptation. It could also be that she was under a great deal of stress, and her judgment was clouded. Maybe she thought Harry was taking her for granted and wanted to get back at him in a very wrong way. Or there could be some dark secret in her past that made her act this way.
Another reason could be that there are some misunderstandings between them. For example, Hermione might misinterpret Harry's actions or words as being too reckless or irresponsible, and she decides to push him away to avoid being dragged into what she perceives as a bad situation. Also, it could be related to her own insecurities. She might feel that she is holding Harry back in some way or that their friendship is becoming too complicated, so she takes the step of pushing him away to simplify things.
One reason could be envy. Hermione is often very good at academics and magic, and Harry and Ron might be envious of her success. For instance, if Hermione always gets top grades in potions class while Harry and Ron struggle, they could lash out at her out of frustration.
One possible reason could be jealousy. Maybe Molly is jealous of Hermione's intelligence and the special bond she has with Harry and Ron. Another reason might be that she feels Hermione is a bad influence on her sons in some way. For example, she might think Hermione's Muggle - born status could bring trouble to the family in the wizarding world which is full of pure - blood supremacist ideas.
One possible reason could be that Hermione wants to pursue her own independent magical research. She is highly intelligent and may feel the need to focus on her studies without the distractions that come with being close to Harry. Another reason might be a disagreement over some major decision in the wizarding world. For example, if Harry has a different stance on how to deal with the remaining Death Eaters or how to reform Hogwarts' curriculum, Hermione, with her strong opinions, may choose to distance herself to avoid constant conflict.
One possible reason could be his Slytherin pride and the long - standing rivalry between Gryffindor and Slytherin. He might have said something mean to Hermione in the heat of that rivalry. Another reason could be jealousy. Maybe Hermione is achieving more academically or getting more recognition, and Draco, being a proud pure - blood, can't stand it.
Another reason could be related to a prophecy. If there was a prophecy in the fanfiction that Naruto would bring great destruction in the future, and Kushina, being a self - sacrificing mother, might think that killing him is the only way to prevent that destruction, even though it goes against her natural love for her son.
One possible reason could be that he has some sort of hidden agenda. Maybe he wants to use Hermione as a bargaining chip later. Another reason might be that there is some magic or force compelling him to do so against his will. It could also be that he has a momentary change of heart, perhaps seeing something in Hermione that reminds him of a past acquaintance or a long - lost bit of humanity within himself.
Harry could be initially confused. He might not understand why Hermione, who has always been there for him, is suddenly pushing him away. So he might try to talk to her to find out the reason.
Maybe they run away because they are tired of the constant danger at Hogwarts. They've faced so many threats, and they just want a break. So they run to a peaceful place where no one knows them.