Perhaps there's a prophecy or some ancient knowledge that Naruto and Sasuke discover. This knowledge reveals that Konoha has been built on a dark secret or is somehow being corrupted from within. Feeling betrayed by their village's true nature, they decide to defect together. They may hope to find a way to purify Konoha or start anew elsewhere without the influence of the corrupt elements in the village.
In fanfiction, it could be due to a new threat that Konoha refuses to take seriously. Suppose there's a new and extremely dangerous enemy on the rise, and Konoha's leadership decides to ignore it or handle it in a way Naruto and Sasuke don't agree with. They might then choose to leave Konoha to face this threat on their own terms, believing that they can't do it while being restricted by Konoha's rules.
Maybe they leave because of a conflict within Konoha. There could be political unrest or a group within the village that they don't agree with. They might think that leaving is the only way to avoid getting involved in something they don't believe in or to protect the village from the inside out in their own way.
It could also lead to some tension. While they have a common goal of leaving Konoha, their individual ideas about what to do next might differ. Sasuke might be more focused on power - seeking ways to become even stronger, while Naruto could be more interested in finding a new place to belong. This difference in priorities could cause some arguments between them, but at the same time, it could also strengthen their bond as they work through these issues.
Another reason might be a lack of acceptance. Despite all his efforts, if Naruto still feels like an outcast in Konoha, he could decide to defect. He might think that he can find a place where he is truly understood and valued elsewhere.
Perhaps he discovers something about his past or his powers that makes him feel he has to leave Konoha to explore it further. For example, he might find out about a hidden place related to the Uzumaki clan and wants to go there alone to uncover the secrets. Or it could be that he has some kind of internal conflict within himself, like feeling unworthy of being in Konoha due to some self - perceived failure, and so he runs away.
Maybe it's due to a misrepresentation of Naruto's character. In the official Naruto series, he is a hero who is deeply connected to Konoha. If the fanfiction shows him in a negative light without proper justification, like suddenly turning against Konoha for no good reason, it could be banned. Also, if the fanfiction involves some sort of political incorrectness within the context of the Naruto universe, such as discriminatory ideas towards certain clans in Konoha, that would be a reason for a ban.
Perhaps they are forced to leave due to false accusations or being framed for something they didn't do. This could create a situation where they feel they have no choice but to leave Konoha in order to clear their names and also protect the village from the real threats that might be lurking in the shadows.
One reason could be to seek a new life away from the constraints of Konoha. Maybe they feel that they can't fully grow or explore their potential within the village. Another reason might be to protect Konoha in their own way. They could believe that leaving and dealing with threats from the outside would keep the village safer.
One reason could be that he feels misunderstood by the villagers. Despite all he has done for Konoha, some still hold grudges or are afraid of his power. Another might be that he wants to explore the world on his own terms, away from the responsibilities and restrictions of Konoha. Maybe he also feels a sense of loneliness there, as he has lost many important people and the village constantly reminds him of those losses.
One possible reason could be fear. Naruto has the Nine - Tails within him, and some in Konoha might be too afraid of its power getting out of control. They may not fully trust Naruto to keep it in check.
One possible reason could be false accusations of a serious crime. For example, if he was wrongly blamed for a major attack on the village. Another reason might be political intrigue. Some powerful figures in the village might see Naruto as a threat to their power and find a way to banish him to maintain their control.