One common reason could be that he finds out the village has been using him all along. Maybe they were only interested in his power as a jinchuriki and not really in him as a person. This realization could lead to his betrayal.
Sometimes in fanfiction, Naruto betrays the village because he falls in love with an enemy of the village. His love for this person could make him question the village's values and ultimately lead to his betrayal. This adds a whole new layer of drama and conflict to the story as he has to choose between his love and his loyalty to the village.
He might be mind - controlled. Some dark magic or an evil character could take over Naruto's mind and force him to act against the ponies in the MLP world.
Sometimes in fanfiction, the plot demands a big twist. So the author makes Annabeth betray Percy to shock the readers. It could be a completely out - of - the - blue reason like she suddenly decides she doesn't like Percy's friends and since he won't abandon them, she betrays him.
It could be that they were misled. For example, they might have been tricked into believing that Naruto was a threat to the village in the future. So, in an attempt to safeguard the village they love, they decided to 'betray' Naruto. This would add a lot of complexity to the story as Naruto discovers the truth later.
One reason could be for comedic effect. It can lead to some really funny situations, like when the guys - turned - girls have to adjust to wearing different clothes or using different bathrooms in the Naruto world.
One reason could be the lack of recognition he gets in the village despite his great contributions. In the fanfiction, Naruto might feel that his efforts to protect the village are taken for granted.
One reason could be that Naruto discovers some dark secrets about the village that make him lose faith in it. Maybe something related to the 'dark sage' in the story reveals a side of the village's history or leadership that he can't accept. Another reason might be that he's framed for a crime he didn't commit, and instead of waiting for the village to believe in his innocence, he decides to leave. It could also be that he feels restricted by the village's rules and wants to explore a different way of being a ninja, which the dark sage figure represents in some way.
Maybe it's to protect the village. He could discover a threat that he can only face away from the Leaf Village, to keep the danger from directly reaching his home and loved ones. He leaves as a form of self - sacrifice.
Perhaps there is a threat that Kakashi has detected, and he believes the best way to keep Naruto safe is to take him out of the village. It could be a group or an individual who is specifically targeting Naruto within the village, and by leaving, they can avoid this danger and also work on finding a solution to deal with the threat on their own terms.
One possible reason could be that he feels misunderstood. In the village, he has always faced discrimination because of the Nine - Tails inside him. People often look at him with fear and suspicion. So, he might run away to find a place where he can be accepted for who he is.
One reason could be poor writing quality. Some fanfictions might have bad grammar, spelling mistakes, or just be very poorly structured. Another reason could be that they deviate too much from the original Naruto story's essence. For example, changing the core personalities of the characters in a way that doesn't seem right. Also, some fanfictions may focus too much on shipping (pairing characters romantically) in a forced or unappealing way.