Perhaps there is a prophecy that Natsu will bring destruction in the future, so the Fairy Tail guild, in an attempt to prevent this, tries to kill him. However, this prophecy could be misinterpreted. It might be that Natsu's power is misconstrued as a threat, when in fact he could be the key to saving the world in a different way. And there could be an outside force manipulating the guild into believing Natsu is dangerous.
Well, it could be related to a power struggle. If Natsu's power grows too quickly and some members of the guild fear he might take over or disrupt the balance within the guild, they could plot to kill him. Also, if there is an enemy who has infiltrated the guild and spread false rumors about Natsu being a threat to the guild's survival, the members might be tricked into trying to kill him.
One possible reason could be a misunderstanding. Maybe Natsu is wrongly accused of a crime he didn't commit, like being framed for causing great harm to the guild. Another could be a dark magic influence. If some powerful dark magic gets into the guild members' minds, they might turn on Natsu without realizing it. Also, it could be a sacrifice situation where the guild believes sacrificing Natsu would save the rest of the world from a great evil.
It could be a rogue wizard who has a vendetta against Natsu and somehow manages to manipulate the Fairy Tail guild. This wizard might have lost to Natsu in the past and is now seeking revenge in a devious way by turning his own guild against him.
One possible reason could be a misunderstanding within the guild. Maybe someone spreads false rumors about Natsu, leading others to believe he's done something wrong. Another reason might be a power struggle. If there are those in Fairy Tail who envy Natsu's strength and popularity, they could plot against him to get him out of the way.
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 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.
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 a misunderstanding within the guild. Maybe some false information was spread about them, leading others in Fairy Tail to turn against them. Another reason might be a power struggle. If Natsu and Erza were becoming too powerful, some jealous members could have conspired to make it seem like they were betraying the guild. Or perhaps an outside force manipulated the situation to drive a wedge between them and the rest of Fairy Tail.
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.
It could be about Natsu having left Fairy Tail for some reason and then reuniting with the guild in a very unexpected way. Maybe he has new powers or a different outlook on life that causes some friction and also some amazing moments of reunion and growth within the guild.
Well, one possibility is that Natsu could join Fairy Tail in a different way than in the original story. Maybe he has some special mission before officially becoming a member. For example, he has to prove his loyalty by helping an elder member with a personal problem.
One possibility could be that Natsu is attacked due to a misunderstanding within the Fairy Tail guild. Maybe a new member misinterprets Natsu's actions as a threat and attacks him in self - defense.