Perhaps Naruto is on a quest to find a way back to his own world. He realizes that staying in Fairy Tail is only delaying his journey. He has a sense of loyalty to his own friends back home like Sasuke and Sakura. So he leaves Fairy Tail, even though he has made some friends there, in order to pursue his ultimate goal of returning to Konoha.
In this fanfiction scenario, Naruto could leave Konoha due to some sort of misunderstanding. Maybe the people of Konoha in the Fairy Tail world suspect him of being too dangerous with his unique abilities. So, he leaves to prove himself elsewhere, perhaps by joining a different guild or team in the Fairy Tail world that is more accepting of his different nature.
One possible plot could be that Lucy and Juvia leave Fairy Tail to go on a self - discovery journey. They might want to explore their individual magic powers more deeply without the constraints of the guild. Maybe they travel to different magical realms, meet new characters, and learn unique magic techniques that they can bring back to Fairy Tail later.
One possible plot could be that Natsu and Erza leave Fairy Tail due to some kind of internal conflict within the guild. Maybe there are differences in opinions regarding how the guild should be run or what kind of jobs they should take. So they decide to set out on their own journey to find a new purpose.
It could be a dark wizard from the Fairy Tail world who sees Naruto as a threat because of his unique powers. This wizard might try to stop Naruto from leaving, fearing that he'll take the knowledge of Fairy Tail's magic to other places.
It could be that there are some internal issues within Fairy Tail that make her leave while being pregnant. For example, there might be a prophecy or a curse that she believes could harm her baby if she stays. So, in order to break free from that potential threat, she decides to leave. Also, she may be facing some personal conflicts with other members of Fairy Tail regarding her pregnancy, like some not being supportive or having different views on how she should handle it, which ultimately drives her to leave.
It could be that Natsu has some sort of falling - out with the members of Fairy Tail. Perhaps there was a misunderstanding during a big mission, and he decides he can't stay any longer. For example, if his actions were misinterpreted and the guild members blamed him for something that wasn't his fault. He might leave to prove his innocence elsewhere.
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.
Well, perhaps in this fanfiction, Naruto is banished due to a false accusation in his world. He lands in the Fairy Tail world and is seen as an outsider. However, his determination and strong will attract the attention of some of the Fairy Tail members. Erza, for example, might see his potential and take him under her wing, training him in the ways of the Fairy Tail magic while he also teaches her some ninja tricks.