It could also be due to personal vendettas against specific individuals in Konoha who have wronged them or their loved ones. If they feel that the village as a whole has failed to punish or prevent these wrongdoings, they might decide to take matters into their own hands and destroy Konoha as a form of revenge.
Perhaps they are being manipulated by an outside force. An enemy of Konoha could deceive them into believing that the village is a threat to the greater good. This would lead them to take the drastic step of destruction. For example, if they are shown false evidence of Konoha planning to start a war that would cause mass destruction, they might act to stop it in what they think is the only way - by destroying Konoha.
One possible motive could be a sense of betrayal. Maybe Naruto felt constantly ostracized in Konoha despite his efforts to be accepted, and over time, that bitterness turned into pure hatred. For example, if he was always treated as an outcast by the villagers even after saving them multiple times, it could drive him to destroy the very place that never truly welcomed him.
It could be due to a prophecy misinterpretation. Suppose there is a prophecy that Naruto misinterprets as the Leaf Village needing to be destroyed for the greater good. Or perhaps he is tricked by a very cunning enemy who convinces him that the Leaf Village is the root of all the problems in the ninja world.
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.
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.
Another motive might be related to some sort of dark influence. Suppose Naruto is exposed to an ancient and evil power that corrupts his mind. This power could fill him with hatred towards humanity, making him believe that destroying all humans is the only way to cleanse the world. Like in some stories where dark magic can twist a hero's good intentions.
One possible motive could be if Sasuke was on a path of destruction that endangered the entire ninja world. Naruto, as the protector of peace, might see killing Sasuke as the only way to stop him. For instance, if Sasuke was about to unleash a powerful and uncontrollable jutsu that would wipe out many innocent lives.
One possible plotline could be that Naruto discovers a deep conspiracy within Konoha that makes him feel betrayed. For example, he might find out that some of the village elders have been using him all along as a tool to gain power. So in his rage, he decides to take revenge on the village. He could start by using his shadow clones to create chaos and disrupt the normal operations of Konoha.
It could also be a power play. In the Naruto universe, power is a big deal. Some might frame Naruto to get him out of the way in their pursuit of power. Since Sasuke has his own group of fans in the fic, they could be used as tools to achieve this by making it seem like Sasuke is against Naruto, when in fact it's all a setup.
One possible motive could be if Sasuke goes too far in his pursuit of power and becomes a threat to the entire ninja world that even Naruto can't reason with. Maybe Sasuke starts to kill innocent people without hesitation, and Naruto, as the protector of the village and the one who believes in peace, sees no other option but to stop him by killing. Another motive could be some kind of dark magic or mind control that makes Sasuke an uncontrollable force of destruction, forcing Naruto to take drastic measures.
One possible motive could be a deep misunderstanding. Maybe Naruto is framed for something he didn't do, and the Konoha ninjas turn against him. In his desperation to prove his innocence and defend himself, he might end up accidentally killing some of them.