Some fanfictions have Naruto uncovering dark secrets about Konoha. These secrets could be about the actions of the previous Hokages or the village elders. Discovering these secrets makes Naruto lose faith in Konoha and start to hate it.
Many fanfictions focus on her forming alliances with outcasts or enemies of Konoha. She might team up with people who also have a grudge against the village in order to seek revenge or change the status quo.
A common plotline could be Naruto returning to Konoha as a powerful and changed individual. He might be hesitant to help the village at first due to his banishment, but eventually, his kind heart prevails. Konoha, in turn, has to grovel and make amends for their past mistake.
I'm not sure of specific 'female Naruto hates Konoha' fanfictions off - hand. You could try searching on fanfiction - dedicated websites like Archive of Our Own or FanFiction.net and use those keywords in the search bar to find relevant stories.
One common plotline is Naruto leaving the Leaf village in anger. He might then team up with former enemies who also have grudges against the Leaf. For instance, he could form an alliance with Orochimaru's followers who also have issues with the Leaf's power structure.
Often, there's a plotline where Naruto and Obito are on opposite sides of a conflict within the fanfiction. Naruto is fighting for the good of the village and Obito is working against it. Naruto's hatred for Obito grows as Obito continues to cause chaos. There might also be a plotline where Naruto discovers some new, even more terrible deeds that Obito has committed, fueling his hatred further.
Some fanfictions might explore how the main characters, like Naruto, deal with the guilt of not being able to protect Konoha. It could show their journey to regain their strength and find a way to bring back their home.
Another reason could be that he witnesses corruption or unfairness within the village leadership. If he sees that the system is rigged against certain groups, including himself or his friends, he could grow to hate Konoha and decide to leave.
One common plotline is Naruto being ostracized by the villagers. They might throw things at him or verbally abuse him. Another is that the ninja academy teachers or higher - ups in Konoha mistreat him, for example, by giving him unfair training or denying him opportunities. Sometimes, Naruto is physically abused by other ninja trainees out of jealousy or because they see him as a threat due to the Nine - Tails inside him.
One common plot could be that the sister has a different ideology. For instance, she might believe in a more radical approach to achieving peace in the ninja world compared to Naruto's more inclusive and forgiving way. This difference could lead to clashes and eventually Naruto's hatred. Another plot could be a power struggle. If the sister is extremely powerful and uses her power in a way Naruto doesn't approve of, like being cruel to weaker ninjas, it could make Naruto hate her.
One common theme could be Naruto feeling betrayed by Konoha. Maybe he discovers some dark secrets about the village that make him turn against it. For example, if he found out that the village was using shinobi unfairly or was involved in immoral activities.