The main antagonist could be an outside force, like a powerful criminal syndicate. They infiltrate the crew by blackmailing or bribing certain members. Their goal is to get rid of Shepard who has been a thorn in their side in their illegal operations across the galaxy.
One possible story could be that his crew is bribed by a powerful enemy. They turn on him during a crucial mission, leaving Shepard alone to face a difficult situation. Maybe they leak his battle plans or deliberately sabotage his equipment.
It might be a rogue ninja from the Wave. They could have a vendetta against Konoha and see Naruto as an easy target to frame and cause chaos between the two places.
A new, original villain could also be the main antagonist. This villain could be someone from Percy's past who has a grudge against him and wants to use the Avengers as a way to get revenge. By making Percy betray the Avengers, this villain can not only harm Percy but also cause chaos among the powerful superhero group.
Maybe there is an evil Pokemon trainer who has influenced Ashley to betray Ash. In this case, that trainer would be the main antagonist. He or she might have promised Ashley something in return for her betrayal, like rare Pokemon or power.
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 new and powerful trainer who manipulates Anabel into betraying Ash. This trainer might be jealous of Ash's success and see Anabel as a means to bring Ash down.
In some cases, it could be an ancient and evil magical being that has been awakened. This being has the ability to manipulate people's minds and convinces everyone that Harry is evil. It wants to isolate Harry before attacking him directly for some unknown but dark reason.
A powerful and envious Pokémon trainer could be the main antagonist. This trainer might be jealous of Ash's bond with Greninja and decides to break it. He could use dark magic or some sort of mind - controlling device to make Greninja turn against Ash.
Another possibility is that there is a false god or a demon that has influenced the true gods to betray Naruto. This false entity could be the real mastermind behind the whole situation. It wants to use Naruto's downfall to gain more power or to bring chaos to the ninja world. So Naruto not only has to deal with the betrayed by the gods part but also has to uncover the true source of this conspiracy which is this false god or demon.
It could be a new character who is jealous of Ash and Skyla's friendship. This character might spread false rumors about Ash to Skyla, causing her to feel betrayed. So, this new jealous character would be the main antagonist.