Maybe the hidden organizations within Konoha that work in the shadows. They could have been involved in some plot against Naruto that led to his decision for revenge. They would be the ones trying to stop Naruto from exposing their secrets and exacting his revenge on the village as a whole.
One possible plot could be that Naruto, after being wronged in some extreme way by Konoha, like false accusations of a heinous crime. He then uses his godlike powers, perhaps newfound abilities he acquired during some hidden training. He might start by targeting the people who directly wronged him, like certain elders or ninja who were part of the conspiracy against him. He could use his powers to expose their misdeeds to the rest of the village before deciding on more extreme forms of revenge.
It could be a new group of rogue shinobi who have been causing chaos in the ninja world while Naruto was away. They might have targeted Naruto's friends or family, which is why he's back for revenge.
The elders of Konoha could be the main antagonists. They are often the ones making the big decisions in the village. If Naruto is seeking revenge, it could be because of their actions, like how they treated him when he was a child or how they might have hidden important information from him.
It could be some hidden members of Naruto's family itself. Maybe there are relatives who have been manipulating things from the shadows and their actions led Naruto to believe he needs to take revenge on the family as a whole.
Sasuke could be an ally. He also has his own issues with Konoha and would understand Naruto's need for revenge. They could combine their powers, with Naruto's massive chakra reserves and Sasuke's unique Sharingan abilities.
Maybe Danzo could be a major antagonist. He's always been a shadowy figure with his own agendas. He might see Naruto as a threat to his secret operations and influence in Konoha, and thus play a key role in getting Naruto executed.
Perhaps there are dark forces from another dimension. These forces might be attracted to Naruto's power and want to either steal it or destroy him to prevent him from using it against them. They could be powerful demons or sorcerers with their own motives.
Another possibility is that the main antagonists could be the leaders of the other ninja villages. They might view Naruto's godlike and rogue status as a danger to the balance of power among the villages. So, they could form an alliance against Naruto, leading to a lot of political intrigue and conflict in the story.
Perhaps it could be a group of bullies from Issei's school days. They used to pick on him and now he's coming back to make them pay.
Madara Uchiha could also be a possible antagonist in this scenario. Even if he is dead in the original story, in a fanfiction, his lingering influence or a resurrected form could manipulate Naruto. Madara was always against Konoha's ideals to some extent and might use Naruto as a tool to destroy what he hated.