It could be related to a prophecy or some ancient rule in the fanfiction world. For example, if there was a prophecy stating that his sister's power would bring destruction if not controlled, Naruto might feel compelled to seal it to prevent chaos.
One possible reason could be to protect her. Maybe she has some special power that attracts dangerous enemies, and Naruto, being the strong and protective character he is, seals her power to keep her safe from those who might misuse it.
It could also be related to her popularity among their peers. If his sister is more well - liked and has a lot of friends, Naruto, who has often been an outcast, might feel envious. He might wish he had the same social skills or charm that his sister has, which allows her to fit in so easily.
One possible reason could be to protect her. Naruto might believe that by leaving, he can draw danger away from his sister. For example, if there are powerful enemies targeting him, he doesn't want his sister to get caught in the crossfire.
Perhaps Naruto was in a situation where he had made a deal. For example, he promised to pay for the seals in exchange for some information about a missing nin or a secret technique. He values knowledge and power, and if paying for the seals was part of getting closer to achieving his goals, he would do it.
Another possibility is that they leave because of a sense of disillusionment. They could have witnessed some corruption or unfairness within Konoha's leadership or among the ninja community. This makes them lose faith in the village and decide to start anew elsewhere.
One possible reason could be fear. Naruto has the Nine - Tailed Fox sealed within him. His clan might have been afraid that this power could bring destruction upon them, so they chose to abandon him. Another reason could be a misunderstanding. Maybe they thought Naruto was somehow in league with the forces that brought the Nine - Tailed Fox to the village in the first place.
It could be that his sister has some special abilities or talents that the family or the village values more. For example, if she has a very rare and powerful bloodline limit, everyone's attention would be drawn to her. In a ninja world, power and potential are highly regarded, so Naruto might be overlooked because his sister seems to have more of that 'special something' at first glance.
In fanfiction, Naruto hating his sister could be due to various reasons. Maybe the writer wants to create a new and complex dynamic. However, in the original Naruto series, Naruto doesn't have a sister, so it's all fictional creation. It could be that the sister character is written to have done something really bad to Naruto or his friends, which makes him hate her in that particular fan - made story.
It could be that there was a prophecy related to his sister that made the family think she was more important. For example, a prophecy that she would be the key to saving the village in the future. And in their short - sighted view, they abandoned Naruto to focus all their resources on her.
The sister could be bullying Naruto out of envy. If Naruto has some special abilities or talents that she doesn't, she might be jealous and lash out at him.
One possible reason could be jealousy. Maybe the sister is more favored by the villagers or has some special abilities that Naruto feels overshadow his own. This could lead to a sense of envy and ultimately hatred.