Maybe Kakashi wants to make Naruto face his past traumas. By hypnotizing him, he can guide Naruto through his memories and help him heal from things like the loneliness he felt as a child or the loss of his parents. It's a way of psychological support through this fictional means in the fanfiction.
One possible motive could be to help Naruto control the Nine - Tails' chakra better. Hypnosis might be a way to reach into Naruto's subconscious and find a way to coexist with the powerful force inside him.
Well, it could be that Kakashi is under some sort of dark spell or curse that makes him see Naruto as a threat to the village. In some fanfictions, there might be a situation where the village's safety is at stake and Kakashi believes that sacrificing Naruto is the only way to save everyone. Also, it could be a case of false information. If someone convinces Kakashi that Naruto has turned evil and is about to cause great harm, he might take the drastic step.
One possible motive could be mind control. Maybe an enemy manages to take over Kakashi's mind and forces him to harm Naruto. Another could be a misunderstanding. For example, if Naruto was thought to be possessed by a powerful and dangerous entity that Kakashi believed could only be stopped by killing Naruto.
Perhaps Sasuke is possessed by some extremely evil entity. And Kakashi, in an attempt to stop the entity from causing more destruction, decides to kill Sasuke. It could also be that Sasuke discovers some dark secret about Kakashi that Kakashi doesn't want revealed, and in a moment of panic and self - preservation, he kills Sasuke.
One possible reason could be that Kakashi is preoccupied with other important matters in the village. Maybe he has some top - secret missions or tasks assigned by the Hokage that demand his full attention, leaving him with little time to focus on Naruto.
One possible reason could be that Naruto might feel Kakashi is too strict with his training. Maybe Kakashi's methods are too harsh for Naruto, making him frustrated and gradually developing dislike.
One possible reason could be Kakashi's reputation as a strict and powerful teacher. Naruto might be in awe of his skills and fear making mistakes in front of him.
One possible reason could be that Naruto might be trying to prove his independence. He has grown and wants to show that he can handle things on his own without always relying on Kakashi's guidance.
Another motive might be related to some dark power corrupting Team 7. This power could have twisted their minds and made them see Kakashi as an obstacle in their path to achieving ultimate power. It could be something like the curse mark in the original Naruto series but even more powerful and insidious.
Yes, there might be some fanfictions like that. In some fan - created stories, Kakashi could use hypnosis as an unorthodox training method for Naruto. It could be a way to help Naruto access deeper levels of chakra control or overcome mental blocks.
One possible reason could be that in the fanfiction, Kakashi might have made a decision during a mission that Naruto strongly disagreed with. For example, Kakashi could have chosen to sacrifice something important to Naruto in order to achieve the overall mission objective.