One possible reason could be that she is forced to for some dark magic related plot. Maybe an evil wizard has put a spell on her that makes her think she has to leave to protect them. Another reason might be that she feels suffocated in her life with Harry and the kids, longing for her old adventurous self and thus decides to abandon them to seek freedom.
One possible reason could be a misunderstanding. Maybe Ginny misinterprets something Harry does and feels she can't stay in the relationship. Another reason might be that she feels overshadowed by Harry's fame and the pressure of being part of the Potter family. It could also be that she has some personal goals or dreams that she realizes she can't pursue while being with Harry and taking care of the kids.
Perhaps he feels betrayed by the wizarding world. Maybe some of his friends turned on him or the institutions he trusted failed him. For example, if the Ministry of Magic wrongly accused him again, it could push him to abandon it all. He may also be haunted by the many deaths he witnessed and feels that leaving is the only way to escape the painful memories.
It could be that the fanfiction writer wants to create some sort of conflict. By having Harry's kids hate Ginny, it adds a new layer of drama to the story. They might be made to believe false things about Ginny which lead to their hatred.
Perhaps they are blackmailed. A powerful dark wizard could threaten to harm all of their friends and family if they don't abandon Harry. They may feel they have no choice but to sacrifice their relationship with their son to protect others they care about.
One possible reason could be miscommunication. Maybe Ginny did something without fully explaining her intentions to Harry, and in the heat of the moment, he yells. For example, if she made a decision about their relationship without consulting him first.
Well, it could be that the fanfiction is trying to show Ginny's jealousy or resentment in a new light. Perhaps she's jealous of Harry's fame or the attention he gets. Or maybe the writer is simply exploring a 'what if' scenario where Ginny and Harry's relationship took a different turn from the start. In the original story, they end up together, but fanfiction allows for alternative storylines, and this could be one of them where Ginny hates Harry for various reasons that might be related to their different personalities, goals or the pressure of the wizarding world around them.
One possible reason could be jealousy. Maybe Ginny sees Harry getting too friendly with another female character in the fanfiction world. Another reason might be differences in their future plans. For example, Harry may be too focused on his Auror duties and Ginny wants more family time.
One possible reason could be miscommunication. Maybe Harry made a decision without consulting Ginny, like joining a dangerous mission. In fanfiction, authors often play with the idea of misunderstandings to create drama. For example, Harry might have thought he was protecting Ginny, but she saw it as him not trusting her enough.
One possible reason could be a growing apart due to their different career paths. Harry, being deeply involved in the wizarding world's security and Ginny having her own Quidditch career. Another reason might be the stress of living in the public eye. Their relationship may not be able to withstand the constant scrutiny and pressure from the wizarding community.
One reason could be that he's tired of the constant danger and politics in the magical world. He might want a normal life away from all the dark wizards and power struggles.