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.
In some fanfictions, it might be due to her association with a so - called 'forbidden' jutsu or knowledge. For example, if she starts to research a jutsu that the village elders consider too dangerous, they could banish her to prevent any potential disasters.
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.
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.
She might leave to find herself. In Konoha, she has always been defined by her relationships with Naruto and Sasuke. Leaving gives her the chance to figure out who she is on her own terms, away from the expectations of her friends and the village.
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 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.
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.
In some fanfictions, it could be due to a misunderstanding. Maybe someone framed Harry for a serious rule violation that Gryffindor's house values highly, like cheating in an important magical exam. And the evidence against him seems so strong that the Gryffindor house decides to banish him.
Maybe he accidentally breaks some ancient and unforgivable rule. For example, he could have uncovered a secret that the gods wanted to keep hidden and in their attempt to silence him, they banish him. In fanfiction, the writers often play with the idea of Percy's curiosity getting him into big trouble with the Olympians.
One possible reason could be that he is wrongly accused of a serious crime against the village. For example, if some important secrets are leaked and the village leaders suspect Naruto without proper investigation, they might exile him to safeguard the village's so - called security.
One possibility is that Sakura leaves Konoha to seek stronger medical ninjutsu training elsewhere. Maybe she's heard of a hidden village with advanced medical techniques and decides to leave her home to master them. This could lead to her facing new challenges, making new friends, and coming back to Konoha as an even more powerful and knowledgeable medical ninja.