One possible reason could be a divergence in values. Maybe in the fanfiction, Naruto discovers that his family was involved in some dark or unethical deeds that go against his principles. For example, if his family was secretly working with an enemy organization that Naruto has been fighting against. Another reason might be a sense of betrayal. If his family had made decisions in the past that put Naruto in a difficult or dangerous position without his knowledge, he could feel the need to denounce them. Also, it could be due to a misunderstanding. False information might be spread about his family, leading Naruto to believe they are not what he thought they were.
In some fanfictions, Naruto might abandon his family due to a false prophecy that convinces him he's a danger to them. He may think that by leaving, he can protect them from harm that might come his way because of his past or enemies.
One possible reason could be a long - held misunderstanding. Maybe Naruto discovers some family secrets that he misinterprets as betrayal or neglect. For example, if he finds out that his family had made some sort of pact that he disagrees with, it could lead to his rejection.
One possible reason could be that he has some unresolved issues from his past, like the absence of his parents during his childhood which made him feel a sense of detachment. Maybe he is so focused on achieving his ninja goals that he unconsciously starts to ignore his family. Another reason might be some sort of miscommunication within the family. For example, if there are secrets that the family has been keeping from him, he might feel betrayed and thus choose to ignore them.
One possible reason could be a misunderstanding. Maybe there was some miscommunication in the past that led Naruto to believe his family didn't understand him. For example, if his family had different expectations for his future as a ninja compared to his own dreams.
It could also be due to a sense of betrayal. If he found out some dark secrets about his family, like his father being involved in something bad that he couldn't forgive. This could make him turn his back on his family and not care about them at all.
One possible reason could be feeling neglected. Maybe his family was always preoccupied with other matters, like protecting the village, and didn't give him enough attention. So he grew to resent them.
A possible reason could be jealousy. If Naruto had a sibling who was always favored by their parents, he might grow to hate his family. He would feel like he was always in the shadow of his sibling and that his family didn't care about him as much.
Perhaps in the fanfiction, Naruto is exposed to a new philosophy or way of thinking that promotes forgiveness. He might meet a wise character who teaches him about the power of forgiving one's family. Also, if Naruto experiences a similar situation where he has to make a tough choice that might be misjudged by others, he could then understand his family better and forgive them. It could also be that Naruto finds out his family had no other option in the situations they were in, and this realization leads to his forgiveness.
One possible reason could be jealousy within the family. If Naruto is getting a lot of attention from others in the harem aspect, his family might feel jealous or threatened. They could then choose to ignore him as a way of expressing their discomfort.
In the official 'Naruto' series, Naruto would never kill his family. However, in some extremely dark and non - canon fanfictions, such fanfictions might exist just for the shock value or to explore extreme 'what - if' scenarios. But this goes completely against the essence of Naruto's character, who values family and friends deeply.