One reason could be that Naruto has seen too much death and destruction in Konoha. His 'godlike' state might make him think that the only way to end all the suffering is to destroy the root cause, which is Konoha. He may believe that Konoha's system is so broken that it can't be fixed and needs to be completely eradicated.
One possible motive could be a misunderstanding. Maybe Naruto discovers some false information that makes him believe Konoha has betrayed him. For example, if he's wrongly led to think that the village elders are planning to harm his friends or his sensei. Another motive could be the influence of a powerful and evil entity that has somehow managed to control Naruto's mind. It could use Naruto's strength to achieve its own goal of destroying Konoha.
One possible plot could be that Naruto is pushed to the brink by the village's constant mistreatment. The Kyuubi, sensing Naruto's anger and despair, influences him to turn against Konoha. They could start by attacking key strategic points in the village, like the Hokage's office and the ninja academy, causing chaos and destruction.
The older generation, like Tsunade, would be horrified. They've seen Konoha through many hardships and would not want to see it destroyed. They would likely mobilize all available forces to stop Naruto and the Kyuubi. Meanwhile, Naruto's friends like Shikamaru and Choji would be in shock. They've always known Naruto as a kind - hearted and loyal friend, and this sudden turn would be very difficult for them to accept. They might initially be in denial and then try to find a way to stop Naruto without harming him.
One popular 'Naruto and Fem Pein fanfic' is 'The World of a Female Pain'. It explores an alternate universe where Pein is female and her interactions with Naruto are quite interesting. It has a unique take on the characters' relationships and the overall Naruto universe.
The plot could involve the child trying to understand Pain's actions. Maybe the child is born after Pain's death and has to face the consequences of his father's actions in the ninja world.
I'm not sure about a specific 'child of pein naruto fanfic'. But you can try searching on fanfic websites like Fanfiction.net or Archive of Our Own. There are a large number of Naruto fanfics there, and you might be able to find one related to this concept.
Perhaps a mind - control situation. Maybe an enemy was able to manipulate Naruto's mind, making him think that Konoha was an evil place that needed to be eradicated. It could be a powerful genjutsu or some other form of mind - influencing technique.
One possible reason could be for his safety. Konoha is a well - protected village with many skilled ninja. She might believe that leaving him there would ensure he has the best chance at survival and growth as a ninja. Also, she may have some mission or obligation that forces her to leave him behind, perhaps something related to the greater good of the village or the ninja world in general.
The 'The Sealmaster of Konoha' Naruto fanfic is likely to be an interesting piece of fan - created work. It probably focuses on a character who is a sealmaster in the village of Konoha. Fanfics like this often explore new abilities, relationships, and storylines within the Naruto universe. For example, the sealmaster could have unique sealing techniques that help in battles or protecting the village.