It could be due to a misunderstanding. Perhaps there was an incident where his sister was involved, but Naruto misinterpreted her actions as something malicious against him. Like she might have accidentally broken something precious of his and he thought it was on purpose.
It also affects his relationships with others. His friends might be caught in the middle of his feud with his sister. For example, Sasuke might see Naruto's hatred towards his sister as a sign of weakness or instability, which could change how they interact. Or Sakura might try to mediate, but Naruto's stubborn hatred could cause problems in their friendship too.
One common plot could be that the sister has a different ideology. For instance, she might believe in a more radical approach to achieving peace in the ninja world compared to Naruto's more inclusive and forgiving way. This difference could lead to clashes and eventually Naruto's hatred. Another plot could be a power struggle. If the sister is extremely powerful and uses her power in a way Naruto doesn't approve of, like being cruel to weaker ninjas, it could make Naruto hate her.
Communication is key. Naruto and his sister could sit down and have an honest conversation about what's bothering him. They could clear up any misunderstandings that led to his hatred.
The story could end with Naruto realizing his hatred was misdirected. After some big event or revelation, he discovers that his brother and sister actually care for him deeply. They all reconcile and become a closer - knit family.
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.
It could be that in the fanfic, Team 7 starts to act in a way that goes against Naruto's moral code. For example, if they start using cruel or unethical methods to achieve their goals. Naruto, being the character he is, would not stand for such behavior and this could lead to his hatred. Additionally, if there is a personal loss that Naruto experiences which he blames on Team 7, that would also contribute to his negative feelings.
One possible reason could be that Naruto's dad was not around during his childhood. In the Naruto story, Naruto grew up alone and ostracized, and he might feel that his dad abandoned him, which could lead to hatred in a 'dark Naruto' scenario.
Perhaps in the fanfic, there is a prophecy that says Naruto's friends will be the cause of his downfall. So, Naruto, fearing for his future and the safety of the village, starts to distance himself from them and eventually hates them. Or maybe his friends accidentally cause the death of someone Naruto loves dearly, which makes him unable to forgive them.