One possibility could be a misunderstanding. Maybe Kakashi is framed for something that makes Naruto believe he has betrayed him. For example, an enemy could use a clone of Kakashi to perform a heinous act, and Naruto witnesses it without seeing the full picture.
Another plot could involve mind control. An evil force might gain control over Kakashi's mind, forcing him to act against Naruto. This would create a tragic situation where Kakashi has no control over his actions, and Naruto is left heartbroken and confused, thinking his mentor has turned on him.
One possible plot could be that Naruto discovers some dark secrets about Konoha's leadership. For example, he might find out that they were involved in unethical experiments in the past. This discovery could make him feel betrayed first, and then lead him to take actions that Konoha sees as betrayal, like refusing to follow orders or even teaming up with an enemy of Konoha who he believes has a more just cause.
However, Naruto also has a big heart. In the long run, he would probably try to find a way to save Kakashi or bring him back to the right side. He wouldn't give up on Kakashi easily, believing that there must be some underlying reason for his actions and that he can be redeemed.
One possible reason could be power. Maybe in the fanfic, there's a new source of power that Tsunade wants desperately and Naruto stands in her way to obtain it. So she betrays him to get to that power.
Another aspect could be related to her past or origin. If she has some hidden memories or a secret agenda tied to her existence as the Fem Kyubii, it could lead her to betray Naruto. For example, if there are some dark forces that are controlling or influencing her from her past, she may be forced to turn against Naruto against her will in a sense.
One possible plot could be a power struggle. Maybe in a world where different fictional universes collide, Naruto God represents a certain power balance. Wonder Woman, perhaps influenced by some external dark force or a misunderstanding of Naruto God's intentions, decides to betray. This could lead to epic battles between their respective allies, with the fate of this combined fictional universe at stake.
The plot could be that Naruto gets a special mission to protect Kakashi's face from a group of rogue ninjas who want to steal Kakashi's identity. Naruto has to use his unique skills to fend off the attackers and keep Kakashi's face safe.
Well, the plot could revolve around Kakashi providing Naruto with a more stable family - like environment. He might cook for Naruto, help him with his studies at the ninja academy in a more hands - on way, and also be there to support Naruto emotionally when he has nightmares about being alone. This could lead to Naruto growing up more confident and perhaps even developing new skills faster as he has someone constantly guiding him.
Well, it could be that in this fanfic, Kakashi discovers a new potential in Naruto. He might train Naruto in some ancient and forgotten ninja arts. This would set Naruto apart from his canon self. Also, their relationship could be explored more deeply, like Kakashi becoming a father - figure to Naruto, and this emotional bond could influence Naruto's growth as a ninja.
A possible plot could be that in a mission gone wrong, Naruto and Kakashi get separated from the rest of the team. They end up in a strange place where they have to rely on each other more than ever. As they face various challenges together, their bond deepens and Naruto realizes his feelings for Kakashi, leading to a kiss.
It could also be a misunderstanding. Hinata might be framed as a traitor. Some false evidence could be planted that makes Naruto and his friends believe she has betrayed them. This would lead to a lot of drama and conflict in the fanfiction as Naruto struggles with whether to believe Hinata or the evidence against her.