Perhaps Naruto has a new power that he doesn't understand and it's making him act strange. This power could be related to some ancient jutsu. As a result, he starts to ignore everyone because he's afraid of hurting them or because he's constantly in a trance-like state due to the power's influence. His friends would then try to figure out what's wrong with him and how to bring him back to normal.
It could be a new, mysterious ninja from a far - off land. This ninja has some sort of mind - control ability and is using it on Naruto to make him ignore everyone. The antagonist's goal might be to weaken the Hidden Leaf village by causing internal chaos through Naruto's isolation.
One possible plot could be that Naruto has been misinformed about Jiraiya's actions. Maybe he heard false rumors that Jiraiya was involved in something bad. So, he decides to ignore Jiraiya out of disappointment. As a result, Jiraiya has to find ways to prove his innocence and regain Naruto's trust.
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 If he was cursed, it could make him withdrawn and cause him to ignore everyone.
One possible reason could be that Naruto sees something in Sai that others don't. Maybe Sai has a unique way of understanding Naruto's pain or his dreams. Another reason might be that Sai represents a new beginning for Naruto. Since Sai has a different background compared to the others, Naruto might find his perspective refreshing and be more drawn to him.
Perhaps Percy has received some bad news or a prophecy that makes him think that by ignoring everyone, he can protect them. So he distances himself from his friends and family, and the fanfiction could explore how they react to his sudden cold - shoulder. They might try to figure out what's wrong with him and how to bring him back to his normal self.
Well, perhaps in this fanfiction, Harry has been through so much that he decides to isolate himself from everyone. He might be tired of the constant danger and the expectations placed on him. So he shuts out his friends like Ron and Hermione, and just focuses on his own inner journey, maybe to discover some new magic that he believes can only be found in solitude.
The plot might involve Naruto being influenced by some external force. For example, a new enemy could be using some kind of mind - control or illusion on him to make him ignore the Rookie 9. Another possibility is that Naruto has become so focused on his training to become stronger that he starts to neglect his relationships with the Rookie 9, thinking that his power is more important for the future of the village.
One possible plot could be that Naruto is shunned by the villagers not just because of the Nine - Tails but also due to false rumors spread by a jealous group. They might constantly bully him, like stealing his food or tripping him in the streets. Naruto, in this fanfic, would have to struggle not only with the physical abuse but also the emotional toll of being alone.
Well, it could be a dark AU (alternate universe) where Naruto is pushed to the brink. Maybe he discovers some great betrayal among his friends and village. So in his rage, he decides to take revenge and starts killing everyone. But this is a very extreme and uncharacteristic concept for the original Naruto character.
Perhaps Naruto gets corrupted by some dark force. It changes his personality completely. He might start seeing all the people in the Hidden Leaf Village as the source of his problems. He could remember all the times he was ostracized as a child and now blames everyone for it. So in the fanfic, his hatred for everyone grows as he views the world in a new, darker light.