In some fanfictions, it might be due to an alternate reality. For example, if there was a different prophecy or a different turn of events at the time Voldemort attacked. Harry could leave his parents to fulfill a new - found destiny in this altered world. Also, it could be because of a miscommunication. A magical misunderstanding might lead Harry to believe he has to leave his parents for their own safety.
Well, in certain fanfiction scenarios, Harry could be lured away from his parents by a powerful magical being who has some sort of ulterior motive. This being could convince Harry that leaving his parents is the only way to save the wizarding world. Or perhaps, in a really complex fanfiction plot, Harry discovers a hidden truth about his family that makes him feel like he has to distance himself from his parents in order to protect them or the wizarding world at large.
One possible reason could be that he might feel abandoned. Growing up without them, he could resent the fact that they left him an orphan. He might think that if they were really so great, they would have found a way to survive and be there for him.
One possible reason could be a misunderstanding. Maybe he discovers some secrets about his parents that he misinterprets. For example, if he finds out they were involved in some dangerous or morally ambiguous activities in their youth that he doesn't fully understand at first.
One possible reason could be that he discovers some long - hidden family secrets that make him question his parents' actions or decisions. Maybe he finds out about some dark deeds in their past that he can't overlook.
One possible reason could be that in the fanfiction, Harry might have discovered some dark secrets about his parents that made him feel betrayed. For example, if he found out they had some hidden and unethical magical experiments in their past.
One reason could be a misunderstanding. Maybe there was a miscommunication between Harry and his friends, and he felt so hurt or angry that he decided to leave. For example, if his friends wrongly accused him of something he didn't do.
Perhaps he discovers some secrets about his parents that he doesn't like. For example, he might find out that they were involved in some dangerous or unethical magic before. This new knowledge could make him angry at them for putting themselves and their family in jeopardy.
One possible reason could be that in the fanfic, the author might twist the story to make it seem like his parents' actions had unforeseen consequences that affected Harry negatively. For example, their fight against Voldemort led to Harry being an orphan and having to bear a great burden from a young age.
Perhaps he leaves in search of a more peaceful life. The wizarding world, despite its magic, has been filled with turmoil for him. He could be seeking a place where he can simply be Harry, not 'The Boy Who Lived' or the hero who defeated Voldemort. He may also be on a quest to discover more about his family's past in the Muggle world, something that has been somewhat overlooked in his life in the wizarding world.
In some fanfictions, Harry might leave his family because of a prophecy or a special mission. He might feel that he has to go it alone in order to fulfill this prophecy or complete the mission successfully. His family might not understand or be able to support him in this, so he decides to leave. Also, there could be jealousy or resentment within the family that makes the environment unbearable for Harry.
Another reason could be a misunderstanding. Maybe he overhears something Harry and Hermione say and misinterprets it as them not wanting him around anymore. So, in a fit of anger and hurt, he leaves. This can lead to a lot of angst and drama in the fanfiction as the other characters then have to figure out how to get him back.