There's a possibility that the main antagonist is a corrupted version of one of Naruto's friends. Some dark force has influenced this friend, and they are now working against Naruto and Kami. Naruto is reluctant to fight his friend at first, but realizes that he has to save his friend from the dark influence. This would create a lot of emotional turmoil for Naruto and make for an interesting story.
Maybe a rogue ninja who has somehow tapped into dark powers related to Kami's domain. This ninja wants to use these powers to take over the ninja world, and Naruto, with Kami's help, has to stop him. In this fanfiction, the rogue ninja could have some personal vendetta against Kami as well, which adds more depth to the story.
Obviously, Kami would be the main antagonist. Since the title says 'naruto betrayed by kami', Kami is the one doing the betraying, which makes him the bad guy in this fanfiction.
It could be a powerful priest or someone who represents the traditional view of kami. They might see Naruto's forsaking of kami as a threat to their power and beliefs, and thus oppose him.
The main character is Naruto, of course. He is the one who meets Kami and Yami. Kami and Yami are also key characters. Kami might be a benevolent figure, perhaps a god - like being, while Yami could be a more shadowy and mysterious entity. Their interactions with Naruto will drive the story forward.
Maybe a rogue ninja who has made a pact with a dark force. This ninja could see Naruto as a threat to his plans of ruling the ninja world, especially with his new status as a dragon warrior of the kami. He would try to stop Naruto at all costs and might have some dark powers of his own.
It could be an ancient evil that Rikudou Sennin once sealed away. With Naruto and Rikudou Sennin meeting, this evil might sense an opportunity to break free and becomes the antagonist.
Maybe a powerful rogue ninja who has discovered a way to steal the powers of divine entities. He sets his sights on Amaterasu and Naruto because he knows that if he can combine their powers, he will be unstoppable. He creates various traps and illusions to separate them and weaken them so that he can carry out his evil plan.
It could be someone who wants to steal Samehada for its power. Maybe a rogue ninja who has heard of Samehada's ability to absorb chakra and plans to use it to take over the ninja world.
It could be a powerful alchemist who has gone rogue and wants to use Naruto's chakra for some dark alchemy purpose.
It could be a jealous gamer who is envious of Naruko's skills and Naruto's natural talent. This antagonist might try to sabotage their progress in the game by hacking or spreading false rumors within the gaming community in the fanfic.
There's a possibility that an evil scientist from another planet could be the main antagonist. This scientist wants to use Bulma's knowledge and Cell's power for his own evil experiments. So he tries to break up their partnership and capture them both for his own purposes. He sends his minions after them and creates various obstacles for Cell and Bulma to overcome.