It could be that Naruto loses someone very dear to him because of Konoha's actions or inactions. For example, if his friends were sacrificed due to the village's political games. This extreme grief and anger might drive him to destroy Konoha in the fanfic.
In a 'naruto destroys konoha fanfic', one possible plot could be that Naruto is pushed to the edge by the villagers' constant mistreatment and the hidden secrets of Konoha's leadership. He discovers some dark deeds that the village elders have been involved in, like using him as a pawn without his knowledge. This betrayal could fuel his anger and lead him to decide to take revenge on Konoha.
Maybe Naruto is under some sort of mind - control in the 'naruto destroys konoha fanfic'. An enemy uses a powerful jutsu to manipulate him, making him believe that Konoha is the source of all evil in the ninja world. So, he starts to attack the village without his true self being in control.
It could be that Naruto is possessed by an evil spirit. This spirit wants to destroy the Leaf Village for its own reasons. Naruto, under its control, would first cut off the village's supply lines, making it difficult for the villagers to get food and resources. Then, he'd start attacking the ninja in the village one by one. He might even use his Nine - Tails chakra in a very destructive way, not caring about the harm it would cause to the place he once called home.
In this kind of fanfiction, Naruto might be banished due to some false accusations or political conspiracies in Konoha. Once banished, he could decide to destroy Konoha out of anger and a sense of betrayal. He may have learned powerful jutsus during his exile and use them against the village that once rejected him.
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.
In such a fanfiction, it would be a very dark and alternative take. Naruto, being godlike, might have been pushed to the edge by something in Konoha, like betrayal or unjust treatment. Maybe he discovers some dark secrets about the village leaders that make him snap.
It could be Sasuke. If he were to turn to the dark side in the fanfiction, his Rinnegan powers could be used to destroy Konoha. He has the potential to be extremely powerful and if he has some sort of vendetta or is influenced by some dark force, he might take his anger out on the village.
The hidden enemies within Konoha who oppose Naruto's ideas of peace and unity could be antagonists. They might spread false rumors about Naruto, turning the villagers against him. This growing animosity between Naruto and the village could result in him lashing out at Konoha, making those who spread the rumors antagonists in the fanfic.
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.
The Hokage, whoever it is at the time, would see Naruto's actions as a major threat. They would likely assemble the ninja forces to defend Konoha. But there would also be a part of them that would wonder what drove Naruto to this. Kakashi, for example, would be conflicted. He has a deep bond with Naruto, but he also has a duty to protect Konoha. So he would try to find a way to end this without harming Naruto too much.
One possible plot could be that Naruto is somehow mind - controlled by a powerful enemy who forces him to turn on Konoha. Maybe the enemy has a special jutsu that can manipulate Naruto's emotions and memories, making him believe that Konoha has wronged him in some way.
Perhaps in this fanfiction, there is a dark prophecy that Naruto misinterprets as Konoha being the source of all evil in the ninja world. So, in his attempt to 'save' the world, he decides to destroy Konoha. Also, it could be that an evil entity has merged with Naruto, and the combined power has a grudge against Konoha for some past event.