The boy could be influenced by outside factors like friends or media and think differently from his parents. Or he could be going through a phase of rebellion to assert his independence.
Sometimes the parents' demands might be unreasonable or not in the best interest of the boy, leading to his disobedience. Another possibility is that the boy might have misunderstood the instructions.
Curiosity could be a reason. Just like in the story I mentioned before, the boy might be curious about something his parents forbid him from doing. For example, exploring a place that is considered off - limits.
Maybe the parents have some mental health issues or are under the influence of a cult. That could make them do such a crazy thing.
Another reason could be that Naruto is lured away by an external force. Some powerful figure or group might convince him that leaving his parents is for the greater good, perhaps in the name of protecting them or the village in a more effective way.
One possible reason could be that in the fanfic, his parents might be depicted as having made some big mistakes in the past that directly affected Harry in a negative way. For example, they could have made a deal with a dark force that put Harry in danger later on.
One possible reason could be that the parents have some unfulfilled desires related to having a girl. Maybe they always dreamed of having a daughter and are trying to create that situation by changing their son's appearance or upbringing. But this is a wrong approach as it doesn't respect the child's identity.
Perhaps Naruto has always felt different from others in the village. And when he finally learns about his parents, he realizes that their actions, even if they were for a good cause like protecting the village, still made his life very difficult. He might be angry that they didn't find a better way to handle things so that he didn't have to suffer so much growing up.
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 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.
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.
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.