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 there's a conflict within the guild that she can't resolve. For example, if there are disputes over the use of certain magic or if she has differences with some of the key members in terms of the guild's future direction. She might decide to leave to avoid the chaos and find her own path.
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.
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 misunderstanding. Maybe someone framed Lucy for something she didn't do, like stealing a powerful magic item from the guild. Another reason might be that she accidentally broke a very important and unbreakable guild rule without realizing it. For example, if there was a rule about not using a certain type of dark magic, and she unknowingly used it to save a friend.
Maybe she just lost interest in the Fairy Tail world. Fanfiction can be a passing fancy, and her enthusiasm might have waned over time.
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.
In a fanfiction, there could be a situation where Lucy is forced to side with a group that Natsu is against. This would make Natsu see her as an enemy. Or perhaps there is a prophecy that Lucy is involved in that Natsu misinterprets as something bad. He might think she is a threat to the guild or his friends. Also, if there is a love triangle situation where Lucy chooses someone else over Natsu in a way that really hurts his feelings, that could be a reason for him to start hating her.
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 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.
Natsu would probably be very confused and sad at first. He's used to having Lucy around, and her sudden departure would leave a big hole in his daily adventures. He might try to convince her to come back immediately.
It could lead to a change in the guild's dynamics. Naruto has his own unique combat style and abilities. His departure might make the guild realize the need to diversify their fighting strategies. For example, they might start to look for members with skills similar to Naruto's ninja techniques.