Perhaps it has to do with a new and mysterious disease. In fanfiction, new and unique diseases can be created. This disease could be something that attacks his unique chakra system, which is different from others. Since his body is so reliant on chakra, if the disease disrupts it enough, it could lead to his death.
In some fanfictions, it could be related to the magical core inside Harry. Maybe his magical core was damaged in some way, and over time, it weakened to the point where his body couldn't sustain itself anymore. Since sleep is a vulnerable state, that's when his body finally gives in. Also, it could be part of a complex plot where the author wants to explore the reactions of other characters to Harry's sudden and unexpected death while sleeping. It can create a lot of drama and angst among the remaining characters in the story.
One possible reason could be to protect Hinata. Maybe Sasuke has unknowingly made a move or decision that Naruto perceives as a threat to Hinata, so he scares Sasuke to make him back off.
Well, it could be for creative exploration. Maybe the writer wants to see how Naruto would turn out if he had a difficult family situation like being abused by his mother. This could then lead to a different path for his relationship with Hinata. It might also be a form of catharsis for the writer, expressing some darker emotions or ideas through this fictional and extreme scenario. Additionally, it could be an attempt to analyze the impact of a negative family environment on Naruto's development in the context of the Naruto - Hinata relationship.
One possible reason could be a powerful curse placed on him. Maybe an enemy with dark magic managed to put a slow - acting curse that is gradually sapping his life force.
Perhaps in this fanfiction, on his birthday, Naruto is targeted by a powerful curse. This curse could be placed on him by a dark sorcerer who wants to end the hope that Naruto represents. As the day progresses, the curse slowly drains his chakra and eventually his life, while his friends are desperately trying to find a way to break it.
It could be due to Sakura's feelings for Sasuke. If she's overly focused on Sasuke and Naruto gets in the way of her plans regarding Sasuke in some way, she might lash out and hurt Naruto without really meaning to cause serious harm.
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 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.
One possible reason could be to gain more power. Maybe he thought that emotions were holding him back from reaching his full potential as a ninja. He might have seen other powerful ninjas who seemed to be emotionless and thought that was the way to go.
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.