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.
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.
Sasuke would most likely side with Naruto. Despite their past differences, they have a deep bond. Sasuke would not let Kakashi harm Naruto without understanding the situation fully. He would step in to protect Naruto and demand an explanation from Kakashi.
Kakashi could use his Earth - Style: Earth Wall jutsu to create a barrier between him and Naruto. This would give him some time to analyze Naruto's new weapon and his changed behavior. He might also use his Sharingan to predict Naruto's moves and dodge the zanpakuto strikes more effectively.
Yes, there are likely fanfictions out there where Naruto has a zanpakuto. Fanfiction writers often like to cross over different anime concepts. They might give Naruto a zanpakuto from the Bleach universe to explore new storylines and character developments. It can lead to really interesting scenarios where Naruto has to learn to use the zanpakuto's powers, which are quite different from the chakra - based abilities in Naruto's original world.
At first, Naruto would be clumsy with it. He has no prior experience with Zanpakuto. But his determination would drive him to practice. He'd study how to hold it properly, how to swing it effectively. Maybe he'd even talk to it like he does with his friends, trying to understand its spirit if it has one.
Maybe it's a mysterious traveler from a far - off land. This traveler recognizes Naruto's potential and strength of character and gives him the three zanpakuto as a means to help Naruto protect his village and the people he loves.
Maybe a zanpakuto with the power to heal. Naruto is all about protecting his friends and village. So a zanpakuto that can heal wounds during battle would be very useful. It could also have a secondary ability to boost the chakra of his allies. This would fit with Naruto's selfless nature.
It could be that the zanpakuto was brought into Naruto's world by some sort of interdimensional rift. Naruto, being curious and always eager to grow stronger, is immediately drawn to it. His godlike perception allows him to sense the latent power within the zanpakuto. He might seek out help from characters who have some knowledge of different power systems, like Kakashi. Together, they could try to decipher the mysteries of the zanpakuto, leading to Naruto adding yet another powerful tool to his already impressive arsenal.
One possibility is that Naruto would be very curious about the zanpakuto. He would start to experiment with it right away. He might try to infuse it with his Rasengan, creating a new and powerful attack. This would be a unique blend of Naruto's ninja skills and the power of the zanpakuto.