The village elders could be the main antagonists. They might see Naruto's godlike powers as a threat to their traditional way of ruling the village and decide to get rid of him. Another option could be a secret organization within the village that wants to use Naruto's power for their own evil purposes and when he refuses, they turn on him.
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 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.
The main antagonists could be some of the conservative Iwa ninjas who oppose Naruto joining their village. They might see him as a threat to their traditional ways and values. Also, there could be some rogue ninjas from other villages who target Naruto because they see him as an easy target now that he's in a new and unfamiliar environment.
The main antagonists could be some of the conservative elders in the Hidden Leaf Village. They banished Naruto in the first place and would see his rebuilding of the Uzumaki clan as a threat to their power. They might try to undermine his efforts by spreading false rumors about him and his new clan.
It could be the ninja from Naruto's former village who don't want him to succeed in his new place. They might see his new - found influence as a threat and try to undermine him.
The main antagonists could be the ones who banished Naruto in the first place. Maybe it was a group of elders in the village who feared Naruto's power and wanted to get rid of him. They would see Naruto as a threat now that he is becoming the Onikage and would try to stop him from returning to the village or causing any changes.
Often, the main antagonists can be the village elders or some corrupt shinobi within the village who are behind their banishment. These characters may fear Naruto and Naruko's growing power and influence.
There could be an outside force, like a neighboring village that wants to keep Naruto and Sasuke away from their own village. They might be afraid of the potential power and influence Naruto and Sasuke could bring back if they return. So, this neighboring village sends their best ninjas to hunt down Naruto and Sasuke during their banishment, making them the main antagonists in the fanfiction.
Well, in this fanfiction, the Akatsuki could be the main antagonists. They would view Naruto's godlike powers as a major threat to their goals. Since Naruto has been trained by Shendu, his abilities would be unpredictable and extremely powerful. They might band together to try and take Naruto down. Additionally, there could be some ancient demons or spirits that are awakened by Naruto's new powers and they see him as an intruder in their realm, so they become antagonists as well. They would use their own dark magic and powers to oppose Naruto.
In this fanfiction, the main antagonists might be a group of dark chakra - users. They are jealous of Naruto's godlike powers and want to take over the empire for their own evil purposes. They could be using dark magic to corrupt some of the people in the empire, turning them against Naruto. There might also be some power - hungry politicians within the empire who are not satisfied with Naruto's leadership and want to seize power for themselves. They would plot behind the scenes to bring down Naruto and take over the reins of the empire.