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.
Perhaps Naruto is pushed to the edge by the constant discrimination he faces in Konoha. Even though he has friends, there are still some villagers who look down on him because he's the host of the Nine - Tails. This continuous negative treatment might build up over time and finally make him snap, leading to the extreme action of destroying Konoha.
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.
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 motive could be that they were somehow brainwashed. Maybe an enemy with powerful genjutsu got to them and made them believe that Konoha was a threat that needed to be eliminated.
In fanfiction, Naruto might kill Konoha if he's under some sort of mind control. Maybe an enemy manages to manipulate his thoughts and turn him against the village. Also, if Naruto experiences a great loss because of Konoha's actions or inactions. Say, if his friends are killed due to Konoha's negligence in protecting them, and he blames the village as a whole. Or if he realizes that Konoha's system is so corrupt that it's causing more harm than good to the world.
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.
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.
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.
Madara Uchiha could also be a possible antagonist in this scenario. Even if he is dead in the original story, in a fanfiction, his lingering influence or a resurrected form could manipulate Naruto. Madara was always against Konoha's ideals to some extent and might use Naruto as a tool to destroy what he hated.
It could be that Kiba has been involved in something that Naruto considers wrong. For example, if Kiba endangered the safety of the village or their friends, Naruto, being the protector - type, would take action against him. Or perhaps there was a misunderstanding between them. Kiba might have been framed for something, and Naruto, believing the false information, tries to 'destroy' Kiba in the heat of the moment.