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.
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.
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.
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.
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.
Well, it could be that the wielder of the Rinnegan has the ability to control powerful forces like the Six Paths techniques. They might use the Deva Path to create massive gravitational pulls that start to crumble the buildings in Konoha. Or perhaps with the Preta Path, they could drain the chakra from all the ninja in Konoha, leaving them defenseless against further attacks, which eventually leads to the destruction of the village.
It could be an evil version of Sasuke. Maybe he has fallen completely to the dark side and manipulates Naruto into destroying Konoha. Or it could be Orochimaru who has found a new way to control Naruto's actions from the shadows.
Sasuke would likely be involved. He has his own issues with Konoha and might side with Naruto, either out of friendship or his own vendetta against the village. Also, the elders of Konoha like Danzo could be important characters as they might be the ones behind Naruto's banishment.
One possible plotline could be that Naruto is somehow corrupted or misled. Maybe he discovers some dark secrets within Konoha that he believes can only be resolved by its destruction. As for the Alvarez Empire, they might see an opportunity to expand their influence in the chaos Naruto creates and form an uneasy alliance with him at first.