There could be a secret organization within the empire itself. They have been secretly controlling things from the shadows for a long time. Naruto's rule threatens their hidden control. They might use dark jutsus and manipulate other powerful figures in the empire to try and get rid of Naruto. They could also create internal unrest by funding rebel groups within the empire.
The main antagonists could be the traditionalist nobles who oppose Naruto's new and inclusive ways of ruling. They might be afraid of losing their power and privilege.
Maybe some rogue ninja clans who want to take over the empire for themselves. They see Naruto as an obstacle to their plans and constantly try to undermine his rule through various attacks and plots. They could also try to turn the people against Naruto by spreading false rumors about him.
It could be rogue ninja groups that oppose Naruto's new way of ruling. These groups might believe that Naruto is trying to take away their freedom and the traditional ways of the ninja world. They could try to undermine his empire by causing chaos and attacking his infrastructure.
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.
The main antagonists might be a new breed of ninja created by some dark jutsu or experiment within the 'dark empire' fanfiction. These new ninjas could have powers that are a threat to Naruto and his friends, and they are bent on spreading chaos and darkness throughout the Naruto world. They might have no moral compass and be solely focused on domination.
One possible plot could be Naruto using his unique ninja skills and leadership qualities to unite a previously divided empire. He might introduce new forms of governance inspired by the values of his village, like equality and loyalty among its people.
The Sound Ninjas could be great antagonists. They could use their own unique parkour - like skills to try and stop Naruto. They might be chasing him through the forest, and Naruto has to use his parkour skills to outmaneuver them.
Maybe some corrupt officials within the prison system itself. They oppose Naruto's more humane and reform - focused approach to prison management. They might try to undermine him at every turn, for example, by cutting off resources or spreading false rumors about him among the prisoners.
Maybe a group of dark - type Pokémon that have banded together and are trying to overthrow Arceus. They view Naruto as an easy target at first, but quickly realize he is a formidable opponent with his ninja skills and new Pokémon - related powers. They would constantly try to undermine Naruto and his efforts to protect the Pokémon world.
A group of troublemaker students might be the antagonists. They could be constantly causing chaos in the school, and Naruto and Sakura have to step in to stop them. These troublemakers might not like the new order that Naruto and Sakura are trying to establish in the high school.
The Hidden Leaf Village elders could be main antagonists. If Naruto turns dark because he feels betrayed by the village, they would be the ones representing the establishment he is against. Their conservative and sometimes self - serving ways could be the catalyst for Naruto's transformation, and then they would be the ones trying to stop him as he becomes a threat to their power and the village's traditional order.
It could be Orochimaru. Even though he was defeated before, he might come back with a new plan. Maybe he wants to use Naruto and Naruko's family for some dark experiment, like trying to extract the unique chakra combination that their family might have.