It could be that the Alvarez Empire has a long - term plan to take over the ninja world. They manipulate Naruto into believing that Konoha is the root of all the problems in the ninja world. Naruto, being naive in some aspects, falls for their lies. As the story progresses, he starts to wreak havoc on Konoha. However, as he realizes the truth, he has to face the consequences of his actions and try to make amends, all while dealing with the Alvarez Empire's true intentions.
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.
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 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.
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, having a fundamental difference in ideology with Sasuke, decides to take a stand. Maybe Sasuke is on a path that Naruto believes will destroy the village or their friends. So Naruto uses his newfound powers, perhaps a combination of Sage Mode and Nine - Tails chakra, to directly confront Sasuke. Naruto could try to break Sasuke's resolve through sheer force and the power of their friendship memories.
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.
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 possible plotline could be that Naruto is somehow mind - controlled. Maybe an enemy uses a powerful genjutsu on him, making him see the Konoha 12 as threats to the village instead of comrades. This would lead to a tragic situation where Naruto, in his altered state of mind, attacks them.
One possible plotline could be Naruto leaving Konoha due to feeling out of place because of the harem situation. Maybe he's overwhelmed by the attention of multiple characters interested in him romantically and decides to seek solitude or a new path outside the village.