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.
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 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.
Another reason could be a rift in their friendship caused by outside factors. For instance, if the wizarding community starts to turn against Harry because of false rumors or misinformation, Hermione might find it too difficult to stand by him. She may fear for her own reputation or safety, and this could lead to her abandoning Harry.
One possible reason could be that Hermione is too focused on her studies and career goals in the wizarding world. She might see a relationship with Harry as a distraction. Another reason could be that she has different values when it comes to love. Maybe she wants someone more like her, who is more into books and intellectual pursuits all the time, while Harry is more action - oriented.
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.
Perhaps Harry was seen spending a lot of time with a new character, a girl who was really good at magic and Hermione suspected that Harry was getting some sort of unfair help from her in terms of academics. It could also be that there were some rumors going around in Hogwarts about Harry having an unfair advantage, and Hermione, being the stickler for rules and fairness, immediately jumped to the conclusion of cheating.
Well, it could be that as time passes in the fanfiction world, Hermione witnesses Harry facing great challenges alone. She might feel guilty for not being by his side and regret her rejection. Also, perhaps she starts to have deeper feelings for Harry that she didn't recognize before, like seeing his bravery in a new light and wishing she hadn't turned him down.
One possible reason could be that Snape, despite his enmity with Sirius, has a sense of duty towards Hermione as a student at Hogwarts. He might not want to see any harm come to her, even if it means protecting her from Sirius. Another reason could be that Snape has his own complex motives and perhaps sees Hermione as an important asset to the wizarding world, so he steps in to keep her safe.
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.
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.