Maybe his sister is involved in a crucial mission from a very young age. Since it's a high - stakes mission related to the safety of the village, the whole village, including Naruto's friends and mentors, are constantly worried about her and give her all the resources and attention. Naruto, on the other hand, is left to fend for himself in his training and development, feeling completely ignored.
One possible plot could be that Naruto's sister is seen as more talented or important in the ninja world. For example, she might be a prodigy in a certain jutsu that Naruto struggles with. So, the village focuses all its attention on her, leaving Naruto feeling ignored. Another could be that she has some special power or connection that makes her the center of attention, and Naruto is constantly overshadowed by her in every aspect, from training opportunities to social recognition.
In the fanfiction, it could be that Naruto's sister has a unique lineage that is highly valued in the village. People are always looking after her, protecting her, and trying to make her the best she can be. Naruto, despite his own efforts and potential, is overlooked because everyone is so preoccupied with his sister. This could lead to Naruto feeling lonely and determined to prove himself without relying on the village's attention.
One possible plotline could be Naruto growing up feeling extremely lonely and trying to find ways to gain his parents' attention even though they're not around. He might start to excel in ninja training not just to prove himself to the village but also in the hope that his parents would be proud if they were there. Another could be Naruto having vivid dreams about his parents and then waking up to the harsh reality of their absence, which could fuel his determination to find out more about them and why they ignored him.
One possible plot could be that they discover they are not actually related in a way that was previously thought. Maybe there was a big misunderstanding about their family relations all along. Another could be a story set in an alternate universe where the social norms are different and such a union is somehow acceptable within that fictional world's rules.
Maybe his parents are dealing with some internal conflicts or secrets. They could be involved in something dangerous or forbidden, and they think that by ignoring Naruto, they are keeping him safe from the consequences of their actions. It could also be that they are under some sort of spell or mind - control that makes them act as if they don't care about him.
One possible reason could be that Naruto has some special power or destiny that his family is afraid of. Maybe they think that being close to him will put them in danger. Another reason could be that there are some misunderstandings within the family. For example, Naruto might have been wrongly accused of something, and his family, without fully understanding the truth, starts to ignore him.
One possible reason could be that his newfound 'godlike' powers make his family feel estranged. They might not understand his sudden transformation and the magnitude of his power, which creates a sense of fear or discomfort, leading them to ignore him.
In some fanfictions, Naruto's sister could be in a coma due to a curse. Naruto discovers a rare herb or a special chakra technique that has the potential to wake her up. He has to overcome many challenges, including political opposition within the Hidden Leaf Village who think he's wasting resources on his sister.
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 this type of fanfic, it could be that Naruto's sister is ill or has some special condition that requires a lot of care from their parents. So, Naruto is pushed to the side. However, Naruto being Naruto, he still tries to find his own way in the ninja world. He might find a mentor outside of his family who sees his potential and helps him grow. Eventually, he could come to terms with his family's situation, or they could realize that they've been neglecting him and try to make amends.
Well, obviously his sister would be a main character. She could be someone with a very different personality from Naruto. Maybe she's more introverted and focused on her studies or training in a very solitary way. Another character could be Naruto's mentor, like Iruka. He might be one of the few people who actually notice Naruto's struggle of being ignored because of his sister, and try to encourage Naruto in his own way.
Naruto might initially feel sad and confused. He could try to prove himself to his friends by working hard on his ninja skills. For example, he might train extra hours to show his friends that he is worthy of their attention.