The main antagonist might be an old enemy of the village who has resurfaced. They see Naruto as a threat to their plans, so they manipulate the villagers into believing Naruto is a traitor. In the harem aspect, they could use the insecurities of the girls in Naruto's life to drive a wedge between them and Naruto. For example, if one of the girls in the harem is from a powerful family, the antagonist could use that family's influence to make her turn against Naruto.
It could be a new character, someone who is jealous of Naruto's growing power and popularity among the girls. This person might spread false information to turn everyone against Naruto. Maybe a rogue ninja who has infiltrated the village and has a vendetta against Naruto for some unknown reason.
It could be the very villagers who once looked up to Naruto. Their betrayal could turn them into antagonists as they might try to further harm Naruto to protect their own interests.
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.
The main antagonist might be an organization that wants to take over the Hidden Leaf Village. They see Naruto as a major obstacle because of his strength and influence among the villagers. So, they devise a plan to make everyone in the village betray Naruto. They use mind - control techniques or spread misinformation on a large scale to achieve their goal. This way, they can weaken the village from within before making their move to take it over.
It could be one of the harem members who has a hidden dark side. Maybe she's jealous of Naruto's closeness to others in the harem and decides to turn the rest against him, so she becomes the main antagonist.
The Ministry of Magic itself could be the main antagonist. They might be so afraid of Harry's growing power and influence that they create false evidence to make everyone believe he has betrayed the wizarding world. They try to control the situation by turning everyone against Harry.
It could be a jealous rival. This rival might have always been envious of Percy's popularity and skills. So, they manipulate Percy's friends into betraying him to get Percy out of the way and take over his position.
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.
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.
In a Naruto betrayed by everyone harem fanfiction, the plot might start with Naruto being framed for a major crime against the village. The harem elements could be that his so - called harem members, who are usually his friends and admirers, are caught in a dilemma. They love Naruto but the evidence against him seems overwhelming. As the story unfolds, Naruto may have to fight not only to clear his name but also to win back the trust of his harem. It could involve him going on a journey to find the real culprit while facing the animosity of his former friends and the village he once loved.
An anti - hero or a morally grey character might be the antagonist. This character could have a different view on relationships and superhero life. He convinces Spider Man that the harem is holding him back from achieving greater things. And Spider Man, being influenced, betrays the harem.