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.
Another motive might be related to power. Suppose Naruto got influenced by some dark force or entity that promised him unlimited power if he would use it to raze Konoha. In the pursuit of this new - found power, he might have lost his moral compass and decided to turn against the village that raised him.
Perhaps it could be due to a false belief. Naruto could have been misled into thinking that Konoha was the root of all the evils in the ninja world. Maybe some enemy cleverly planted false evidence or memories in his mind, making him believe that by destroying Konoha, he would be saving the entire ninja world from a greater threat.
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.
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 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.
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 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.
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 such a fanfiction, it could be possible through a dark corruption of Naruto's power. Maybe the Nine - Tails' influence takes over him completely. His powers could go out of control, and with his incredible strength, he might start attacking without restraint, believing that the current world is beyond saving or redemption.