It could be homesickness. Naruto has deep roots in his own world, with friends like Sasuke and Sakura, and his sensei Kakashi. In the Fairy Tail fanfiction world, no matter how interesting it is, it's not his home. He may constantly miss his own village, the Hidden Leaf, and all the familiar places and people there, which eventually leads him to leave.
Maybe it's due to power differences. Naruto has his own set of unique and powerful jutsu. In the Fairy Tail universe, magic is the main form of power. He could feel that his powers are not being utilized or respected in the right way. He might also be frustrated with the lack of understanding of his ninja skills among the Fairy Tail members, so he chooses to leave.
One possible reason could be a conflict of power. Naruto has his own set of powers from the Naruto universe, like chakra and jutsus. In Fairy Tail, magic is the main power source. Maybe his powers were seen as a threat or too different, causing the guild to force him out. For example, if his chakra-based attacks were disrupting the magical balance in Fairy Tail's world.
One possible reason could be that she feels she has outgrown the guild. Maybe she wants to explore new magic on her own and believes the Fairy Tail environment has become too comfortable and is hindering her growth.
Perhaps they leave because of a disagreement within the guild. Maybe there's a new policy or a decision made by the guild master that they don't agree with. For example, if the guild decides to get involved in a war that they think is unjust, they might choose to leave rather than participate against their beliefs.
One possible reason could be to seek new adventures. They might feel they've reached a point in Fairy Tail where they've done all they can and want to explore new magic and challenges elsewhere. For example, they could have heard of a far - off land with a different type of magic that they are eager to learn about.
It might be due to the fanbase loyalty. Fairy Tail fans are really into their own world and characters. They might not want to introduce Naruto elements as they feel it could disrupt the original charm of Fairy Tail. Also, the art styles are different. Naruto has a more traditional Japanese anime look, and Fairy Tail has its own style. This visual difference could be a reason for the lack of crossovers in fanfictions.
One possibility is that they leave to explore a new land filled with unknown magic. They might be on a quest to find a powerful magic item that could help Fairy Tail in the future.
One possibility could be that they leave to seek greater magical power. Maybe they've heard of a mysterious land filled with powerful magic and they decide to embark on a journey together. They leave Fairy Tail behind in order to become stronger and return to protect their guild in a more powerful way.
One possible plot could be that Naruto is somehow transported to a world where Saiyan powers and Fairy Tail magic exist. He might start off as an outcast, not understanding these new powers at first. But as he trains and learns, he combines his ninja skills with Saiyan strength and Fairy Tail magic to become a powerful force and fight against an evil that threatens all three aspects of this new combined world.
Well, perhaps in this fanfiction, Fairy Tail characters bully Naruto because they are jealous of the attention he gets from certain characters in their shared universe. They start by making fun of his appearance, like his orange jumpsuit, and then escalate to more mean - spirited pranks, like using their magic to disrupt his ninja training.
Well, it could be that in this fanfic, Naruto is somehow transported to the Fairy Tail universe. And due to his different power set and origin, the Fairy Tail members misunderstand him and think he's a threat. Maybe they see his shadow clone jutsu as some sort of dark magic and turn against him.