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.
It could also be due to outside influence. If there is a powerful dark force or a manipulative character in the fanfiction that convinces Harry that his parents are not what he thought they were. They might make him believe that his parents' actions led to some great harm that he can't overlook.
One possible plotline could be Harry feeling extremely lost and alone at first. He might have to find a new place to live, perhaps with the help of his friends like Ron and Hermione. He could struggle with self - worth, constantly wondering what he did wrong to make his parents disown him.
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 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.
They could have been disowned if they took a stance on a political or magical issue that was against their parents' beliefs. For instance, if there was a conflict between pure - blood and half - blood wizards, and Harry and Ginny sided with the half - bloods when their pure - blood parents were firmly against it. This difference in ideology could cause a rift so large that their parents would disown them.
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.
It could also be due to a prophecy. Suppose there's a prophecy that Naruto will bring great disaster in the future. His parents, believing in the prophecy, might decide to disown him in an attempt to avoid that future. They might think that by cutting ties with him, they can somehow change the course of events.
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 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.
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.
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.