Another reason could be political. There might be different factions within Fairy Tail. Some members could be jealous of Naruto's popularity or strength. They could have spread false rumors about him, which led to the decision of forcing him to leave. It's not uncommon in fanfictions for internal guild politics to play a role in such situations.
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.
Perhaps it was a misunderstanding. Naruto is known for his impulsive nature at times. He might have accidentally broken some important Fairy Tail rules without realizing it. Like he could have unknowingly used a jutsu that was misinterpreted as a form of dark magic in the Fairy Tail world. And as a result, they made him 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.
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.
The overall mood of the story would change. It would become more somber. There would be a sense of loss. And it might lead to a quest to bring Naruto back. Maybe some of the Fairy Tail members would go on a journey to prove Naruto's innocence or to find a way to make the guild accept him again. This would open up new story arcs and adventures in the fanfiction.
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 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.
One possible reason could be false accusations against him. Maybe he's wrongly blamed for a crime he didn't commit, like being framed for a major attack in the village. This would lead the village leaders to force him out to maintain 'peace' and security.
Perhaps there have been disputes between the fanfiction community and the official Naruto representatives. For example, if the fanfiction community has been misusing or over - exploiting the Naruto character in a way that goes against the spirit of the original work. This could lead to the decision of asking Naruto to be removed from fanfiction.
Perhaps continuous disappointment. If all his efforts to bring peace and unity were constantly thwarted, like his attempts at forging alliances between different ninja clans being undermined time and again. This build - up of frustration might lead him to snap and decide to leave in search of a new way or place where his ideals could be realized.
One possibility is that the guild would experience a significant emotional impact. Lucy is a central figure, and her celestial spirit magic has been crucial in many battles. Juvia, with her water magic, is also a strong member. Their departure might lead to a decrease in the guild's overall power. Some members might feel betrayed, while others could be motivated to find out why they left and try to bring them back.