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.
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.
In a few fanfictions, it could be a jealous ninja within the village. Maybe someone who has feelings for Naruto and sees Sakura as an obstacle. This ninja could create a false narrative that leads to Sakura's banishment, thus becoming the main antagonist in the story.
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.
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 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.
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.
The village elders could be antagonists. They might see Naruto and Kakashi as threats to their traditional way of ruling the village and use false accusations to banish them.
In this kind of fanfiction, the Fallen Angels could be main antagonists. They might see Naruto and Sasuke as threats to their plans in the DxD world.
In some fanfictions, a new character could be created as the main antagonist. This character might be jealous of Naruto and female Sasuke's growing relationship and power. They try to create rifts between them and stop them from achieving their goals.