One possible reason could be that she is wrongly accused of a serious crime she didn't commit. For example, if there was a major theft in the village and false evidence was planted against her. Another reason might be that she has some new and powerful abilities that the village elders fear. They may think she could become a threat in the future, so they banish her to protect what they see as the village's stability.
Perhaps she discovers some dark secrets about the village. Secrets that the higher - ups in Konoha don't want to be exposed. To keep her quiet, instead of silencing her in the village which might cause more suspicion, they banish her. This way, they hope she will be far away and unable to spread the word about what she has found.
One possible reason could be false accusations of a serious crime. For example, if he was wrongly blamed for a major attack on the village. Another reason might be political intrigue. Some powerful figures in the village might see Naruto as a threat to their power and find a way to banish him to maintain their control.
One possible reason could be fear. Naruto's 'godlike' powers might be too much for the village to handle. They could be afraid that he might accidentally cause destruction. Another reason might be envy among some of the villagers or ninja. They may not like that Naruto has become so powerful all of a sudden and want him out of the way.
One reason could be his power. His connection to the Nine - Tails makes him extremely powerful. In fanfiction, some in Konoha might fear this power and thus hate him. Another reason could be jealousy. Naruto becomes very popular and respected in the original story. But in fanfiction, some characters might be jealous of his achievements and turn that into hatred.
One possible fanfiction idea could be that Naruto is wrongly accused of a heinous crime against Konoha. The village elders, fearing his power and influenced by some anti - Naruto factions, sentence him to death. However, instead of executing him, they banish him. Naruto, heartbroken and confused, leaves Konoha with a vow to find the truth and prove his innocence. He embarks on a journey, meets new allies who believe in him, and gradually grows stronger, all while plotting his return to clear his name.
To change her character dynamics. In fanfiction, if she's not from Konoha, her relationships with characters like Naruto and Sasuke will be different. Maybe she has a different loyalty or a different set of goals that are not related to Konoha's well - being.
Maybe in the fanfiction, there were some political motives. Hiruzen might have been pressured by other hidden villages. They could have threatened Konoha if Naruto, as the Nine - Tails' jinchuriki, remained in the village. So, to avoid a potential war or conflict, Hiruzen made the difficult decision to banish Naruto. Also, it could be due to a misunderstanding. Naruto might have been in the wrong place at the wrong time during an incident, and Hiruzen misjudged the situation.
One possible reason could be for the protection of the village in a very extreme and controversial way. Minato might think that Naruto's presence is attracting too much danger and decides to banish him to keep the village safe.
One possible plot could be Naruto leaving Konoha and then training intensively in isolation. He might discover new powers or techniques that he didn't have the chance to explore before. Another plot could be Naruto forming alliances with other outcasts or villages that were once enemies of Konoha. He could then use these newfound relationships to prove his worth and show Konoha that they made a mistake in banishing him.
Another reason might be related to Naruto's loyalty being questioned. In fanfiction, there could be a plot where an enemy tricks the guild into believing Naruto has betrayed them. The Fairy Tail guild values loyalty highly, and if they think Naruto has sided with an enemy, they might banish him. For example, if an enemy uses some sort of illusion magic to make it seem like Naruto has attacked a guild member, this could lead to his banishment.
One possible reason could be a false accusation of treason. Maybe some false evidence is planted against her, making the village leaders believe she's a threat. So they banish her.