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.
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.
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.
A plot could involve the Leaf Village betraying Naruto when a powerful and ancient curse is placed on him that makes him seem like a mind - controlled puppet of a great evil. The village, in its panic, decides to take preemptive action against Naruto without fully investigating. This could lead to Naruto having to fight not only the external forces that are trying to use the situation to their advantage but also his own former comrades from the Leaf Village who are now hunting him down.
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.
The plot could involve Naruto coming back to the Leaf Village to fulfill a prophecy. He may have discovered something during his travels that made him realize he has a crucial role to play in the village's future. Along the way, he could face challenges from within the village, like some people being skeptical of his newfound knowledge or power. But through his determination and the bonds he has with his friends, he overcomes these obstacles and helps the village thrive.
Maybe it's to protect the village. He could discover a threat that he can only face away from the Leaf Village, to keep the danger from directly reaching his home and loved ones. He leaves as a form of self - sacrifice.
In one possibility, Naruto might leave the Leaf due to a misunderstanding. For example, if the villagers continue to show distrust towards him despite his efforts. He could set out on a journey to find a place where he truly belongs. Maybe he meets some new allies on his way, people who understand him without any prejudice.
The village might experience a huge boost in morale. Naruto killing Pain would be seen as a major victory, and the villagers would feel safer. They would look at Naruto as an even greater hero, which could lead to more trust and unity within the village.
One possible motive could be to use Naruto as a bargaining chip. Itachi was a complex character with his own goals related to the safety of the Hidden Leaf Village in some ways. He might have thought that by kidnapping Naruto, he could influence the village's decisions. For example, he could try to stop certain actions the village was planning that he believed would lead to more harm. Another motive could be related to the Nine - Tails within Naruto. Itachi might have wanted to study or control the power of the Nine - Tails for his own purposes, perhaps thinking it could be a way to protect Sasuke in a different manner.