One possible reason could be that he accidentally causes a great deal of destruction during a mission that the guild can't overlook. Maybe he loses control of his dragon slayer magic and wrecks an important building or site, leading to his expulsion as a form of punishment.
In some fanfictions, Natsu might be framed for a crime he didn't commit within the guild. Another wizard could set him up, making it seem like he stole from the guild's treasury or betrayed a fellow guild member. As a result, the guild leaders, believing the false evidence, expel him.
One possible plotline could be Natsu trying to prove his innocence. Maybe he was wrongly accused of a serious crime within the Fairy Tail guild, like endangering the lives of other guild members during a mission. He then sets out on a journey to find evidence that clears his name while also facing various challenges and enemies along the way.
One possible reason could be that he accidentally causes too much destruction during a mission. Maybe he loses control of his magic and wrecks an important place in the magical world, leading the guild to expel him as a form of punishment.
One reason could be that the fanfictions don't match his view of the Fairy Tail world. He has his own understanding of the guild, his friends, and their adventures, and when fanfictions deviate from that, he doesn't like it.
One reason could be that some writers might want to create a more complex or darker storyline. By having Natsu be hated, it adds conflict. Maybe they portray him as having made a big mistake that the other characters in the fanfic can't forgive.
One reason could be that the fanfiction author is trying to create a new and edgy storyline by making Natsu a more negative character. But this often doesn't sit well with fans who love the original positive and passionate Natsu.
They could leave for a quest of self - discovery. Natsu might want to learn more about his past, especially about his dragon, and Juvia could be looking to find out more about her water magic's origin. So they leave Fairy Tail to explore different places and meet various mages who might have the knowledge they seek.
Perhaps Natsu is under the influence of a powerful and dark magic that makes him lose control of himself and accidentally hurt Lucy. It could also be that Natsu is trying to protect Lucy from something but his actions end up causing her harm instead. Like if he tries to keep her away from a dangerous situation by pushing her too hard and she gets injured.
It could be a rival wizard from another guild. This wizard might be jealous of Natsu's power and popularity within Fairy Tail. So, they fabricate evidence to get Natsu expelled, aiming to not only remove him as a competitor but also to create chaos within Fairy Tail. They could continue to be a thorn in Natsu's side as he tries to clear his name and get back to the guild.
One possible reason could be that he was wrongly accused of a serious crime within the guild. Maybe some powerful and influential members believed he was a threat and pushed for his banishment. For example, if there was a string of mysterious attacks and Natsu was framed as the culprit due to his often wild and uncontrollable nature in battle.
One possible reason could be a conflict with other guild members. Maybe there's a misunderstanding or a fight that makes Natsu feel he no longer belongs. Another reason might be that he has a personal mission that goes against the guild's rules or values in the fanfiction. He could also be framed for something he didn't do and, feeling betrayed, decides to drop out.