The plot could be that Naruto discovers a dark secret about his family that makes everyone in the village fear and reject him. For example, if it was thought that his father was responsible for a great tragedy. Naruto would then struggle to come to terms with this new information while also trying to regain the trust of those around him. He might find allies in unexpected places, like some of the outcast ninja from other villages.
One reason could be a misinformation campaign. Some malicious wizard or witch might have spread false rumors about Harry, making everyone believe that he has done something terrible like being in league with Voldemort again.
Naruto would likely become more withdrawn at first. He's used to being an outcast to some extent, but total rejection would hit him hard. He might start to question his own worth and his dreams of becoming Hokage. However, as time goes on, he could develop a stronger sense of self - reliance. He'd have to rely on his own skills and instincts more, which would make him a more formidable ninja in the long run.
It might refer to a fan - created story in the Naruto fandom that was turned down. This could be due to various reasons. For example, if it contained offensive content towards the original characters or if it deviated too much from the overall theme and feel of the Naruto series. It could also be that the writing style was simply not engaging enough for the reviewers or the audience it was intended for.
Perhaps Harry tries to find the root cause of the rejection. He might start investigating if there's some sort of dark magic or false rumor spreading about him that has made everyone turn against him. He could question his closest friends or even seek out the help of some of the more reclusive teachers at Hogwarts to figure it out.
One consequence could be an imbalance in the world's population. There might be too many people for the existing resources, leading to shortages of food, water, and living space.
It could be that his new 'godlike' power has isolated him. People might be either in awe or afraid of him, and he may feel that he can't be close to others as before. So he acts coldly as a defense mechanism.
It could be Sasuke. Maybe Sasuke is in a bad mood on Naruto's birthday and rejects Naruto's invitation to hang out or something. Since they have a complex relationship, Sasuke's rejection would really hit Naruto hard.
Well, in some fanfictions, Naruto might use some super powerful jutsu that he either discovers or creates. Maybe it's a new form of the Rasengan combined with some sealing techniques. It could also be that he taps into some ancient power or makes a deal with some sort of god - like entity within the Naruto universe.
Maybe he got some kind of curse. In the Naruto universe, there are all sorts of dark magic and curses. If he was cursed, it could make him withdrawn and cause him to ignore everyone.