Perhaps she has fallen in love with someone outside of Konoha who can't or won't go there. Love can be a very strong motivator. If her partner has a history with Konoha that makes it impossible for them to be there, she may choose to stay away from Konoha to be with that person.
One reason could be that she feels betrayed by Konoha. Maybe she has faced discrimination or unfair treatment there in the past because she's female in a world that might be more used to male ninjas. For example, she could have been passed over for important missions or training opportunities just because of her gender.
Perhaps Naruto has been pushed too far by the villagers' continuous mistreatment. Even though he has saved them multiple times, they still show hostility or indifference towards him. So, in the fanfiction, he decides not to help Konoha anymore as a form of self - protection and to break free from this one - sided relationship.
On a larger scale, it could change the balance of power in the ninja world. If Fem Naruto has some unique abilities and she's not on Konoha's side, other villages might try to recruit her or use her absence to their advantage. This could lead to more conflicts between the villages and a re - evaluation of alliances in the Naruto universe.
One possible reason could be that Naruto is extremely powerful and his skills are needed to protect Konoha from a new and powerful threat. His combat abilities, like his Rasengan and Sage Mode, are crucial for the village's defense.
Perhaps Naruto has found a new purpose or community outside of Konoha that values him more. He may be so content with his new life that he simply doesn't want to get involved with Konoha's problems anymore. Konoha's actions towards him could have made him realize that his loyalty was misplaced all along.
One possible reason could be that Naruto feels betrayed by Konoha. Maybe he discovers some dark secrets about the village's leadership or past actions that make him question whether Konoha is truly worth saving. For example, if he finds out that they were involved in unethical experiments or unjust treatment of certain clans. Another reason might be that he has been pushed too far by the villagers' continuous mistrust and discrimination towards him, despite all he has done for them. So he decides he's had enough and refuses to save the village that has not fully accepted him.
One possible reason could be that Naruto feels betrayed by Konoha. Maybe he discovers some dark secrets about the village that make him question whether it's worth protecting. For example, if he finds out that the village elders were involved in unethical experiments or unjust actions against certain groups. Another reason might be that Naruto has different ideals now. He could believe that there are more important things in the world than just protecting Konoha, like bringing true peace to all nations without focusing on one village's interests.
One possible plot reason could be discrimination. In the Naruto world, there are often biases against those with different abilities or appearances. If Fem Naruto is constantly facing unfair treatment in Konoha due to her being a female version of Naruto, she might decide to leave. For example, she may not be given the same opportunities as male ninjas in training or missions. Another reason could be a search for identity. Maybe she feels that she can't truly be herself in Konoha and needs to go on a journey to discover who she really is away from the village that has so many expectations of her.
It could also be that Naruto has grown disillusioned with the politics in Konoha. Constant power struggles, nepotism, or unfair treatment of certain groups within the village might have pushed him away. He might feel that his help would only be enabling a corrupt system.
One possible reason could be that they need his power. Naruto is extremely powerful, and Konoha might be facing a new threat that they believe only Naruto can help deal with. For example, a powerful enemy from outside the village might be on the verge of attacking, and Naruto's combat skills and unique jutsu are crucial for the village's defense.
One possible reason could be feeling ostracized. In the Naruto world, being different is often not easily accepted. As a female Naruto, she might face even more scrutiny and prejudice. Maybe she's tired of the constant expectations and the way she's treated in Konoha, so she decides to run away to find a place where she can be herself.