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.
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 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 miscommunication. Maybe Hermione is so caught up in her own thoughts and studies that she accidentally snaps at Harry without realizing how harsh she is. For example, she might be under a lot of pressure to do well in her classes and Harry's requests for help or just his presence might seem like an annoyance at that moment.
It could be that she sees the pain she caused Harry and it makes her feel guilty. In the story, perhaps she was influenced by others' opinions of Harry and didn't trust her own long - standing friendship with him. When she finally comes to her senses, she regrets all the hurtful things she said or did.
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.
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.
One possible reason could be her involvement in the wizarding world. If her parents are muggles and they find out about the extreme dangers she faces in the magical realm, they might disown her out of fear for her safety. Another reason could be if she starts to show more loyalty to the wizarding community than to her muggle family, making them feel like she no longer belongs with them.
In fanfiction, she could be injured during a battle against dark wizards. Maybe she was caught off - guard while trying to protect her friends.
One reason could be his status as the Boy Who Lived. In the original story, Harry has this special aura about him, and in fanfiction, Hermione might be drawn to that in an obsessive way. Also, his bravery and leadership qualities could be factors that make Hermione overly interested in him.
One possible reason could be that he's been influenced by some dark magic or a spell that makes him act out of character. Another reason might be extreme jealousy, say if Hermione is getting more recognition in the wizarding world than him for some time and he lashes out in a moment of weakness.