It could be due to political reasons. His clan might have been trying to protect their own status within the village. Having Naruto, with the dangerous power he carried, associated with them could have put their standing at risk. So, in order to preserve their influence and avoid potential persecution from other clans or the village leadership, they abandoned him.
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.
Perhaps it was a cultural or traditional belief within the clan. They might have had a strict code regarding those who carried such a powerful and potentially dangerous entity within them. Naruto's situation violated some fundamental tenet of their beliefs, and as a result, they abandoned him to uphold their clan's values and way of life.
In this fanfiction, Naruto could reject his clan because of the dark secrets or past actions of the clan. He is a character who values justice and friendship. If the clan has a history of wrongdoings that he discovers, he may not want to be associated with it. Also, Naruto has his own dreams and goals that might not fit within the framework of the clan. He has always been a bit of a rebel, and rejecting the clan could be his way of standing up for what he believes in.
One possible reason could be to seek greater power and training opportunities elsewhere. Maybe he feels restricted within his clan in terms of the type of jutsu he can learn or the level of training he can receive. So, he decides to leave to explore different ninja arts and grow stronger on his own terms.
One reason could be that his team discovers some kind of hidden power in Naruto that they fear. Maybe they think he's too dangerous to be around, so they abandon him. Another possibility is that they are influenced by some outside force, like an enemy who convinces them that Naruto is a liability.
Perhaps there were some dark secrets in his clan that he discovers. These secrets could be related to past wrongdoings, like how they treated other clans or individuals. If Naruto has a strong sense of justice, learning about these things might make him hate his clan. It could also be that he feels ostracized or different within his clan, like if he has abilities or beliefs that are not accepted by the majority of the clan members.
One possible reason could be that the clan fears his power. In some fanfictions, Naruto's growing strength and his potential to disrupt the clan's traditional power structure might lead to his exile. They may see him as a threat to their established ways.
It could be due to a misunderstanding. Kakashi might think that Naruto is getting involved with something dangerous or has some potential that he can't handle. So, in his warped way of thinking, he abandons Naruto to protect him from himself or from some unknown danger.
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.
Well, one possible plot could be that Naruto is shunned by his clan due to some false accusations. Maybe they think he has some dark power within him that could endanger the clan. So, they cast him out, leaving him to fend for himself. This would lead to Naruto having to prove his worth on his own, without the support of his clan, and he might start to develop a more independent and self - reliant personality.
Perhaps the Konoha leadership made a bad decision. They might have thought that distancing themselves from Naruto would be better for the village's overall image. Or they were influenced by some elders who held grudges against Naruto's father and took it out on Naruto.
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.