In this fanfiction, perhaps Naruto could be under some sort of mind control. Maybe an enemy has found a way to manipulate him into attacking the Leaf. It could also be a case where Naruto is misled about the true nature of the Leaf Village, believing it has committed some great wrong that warrants his attack.
One possible plot could be that Naruto has a vision of a future where the Leaf Village causes great harm to the ninja world. So, in an attempt to prevent this future from coming to pass, he decides to attack the Leaf in order to dismantle it before it can do any damage. This would put him in direct conflict with his friends and former comrades, creating a lot of drama and internal struggle for Naruto as he battles with his loyalty to the village and his sense of justice.
It could be an old enemy who has resurfaced and found a way to turn Naruto against the Leaf. Maybe Orochimaru, who has always been interested in Naruto's power, manipulates him into attacking the village. Orochimaru could use his knowledge of dark jutsu to influence Naruto's mind.
One possible plot could be that Kakashi is under a genjutsu. In this fanfiction, an enemy ninja might have cast a powerful genjutsu on Kakashi, making him see Naruto as a threat to the village. So, Kakashi attacks Naruto, but Naruto, being the understanding person he is, tries to break the genjutsu instead of fighting back right away.
In this fanfiction scenario, it could be that the zanpakuto has a mind of its own. It takes control of Naruto and forces him to attack Kakashi. The zanpakuto might be from a different dimension and is trying to create chaos in the Naruto world. Kakashi would have to rely on his ninja skills and his knowledge of various jutsu to counter Naruto's attacks and find a way to free Naruto from the zanpakuto's control.
Perhaps there's a time - travel element involved. Naruto from the future, who has been through some horrible experiences, travels back in time and, in a state of confusion or rage, attacks Kushina. Or it could be that a powerful villain has the ability to manipulate Naruto's emotions and uses that power to make him turn on his mother. This would create a very complex and dark plotline that challenges the normal Naruto narrative.
One possible reason could be a misunderstanding. Maybe Naruto is somehow influenced by an enemy's jutsu that makes him see Minato as a threat. For example, if an enemy uses a genjutsu to distort Naruto's perception of his father.
Well, perhaps in this fanfiction, Naruto left because he felt unappreciated in the Leaf. But then the Leaf discovers some secrets or powers that are tied to Naruto. They start to see all the good he has done in the past and make a big effort to bring him back. They might hold a big ceremony to welcome him and show how much they truly value him now.
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.
One idea could be that Naruto is under a powerful genjutsu that makes him see Konoha as an enemy. So, he attacks without realizing it's his home. Another could be that an evil entity has possessed Naruto, forcing him to turn against Konoha. It might also be that Naruto has been misled by false information about Konoha's dark secrets and decides to take action against it.
In fanfiction, the idea of Naruto attacking Kushina is very uncharacteristic as they are mother - son. It could be a very dark or alternate universe scenario. Maybe in a plot where Naruto is mind - controlled or in a completely warped reality where family bonds are reversed.
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.