In a more futuristic world, a corrupt corporate leader could be the bad guy. He wants to use Naruto's abilities for his own profit, like making Naruto fight in illegal gladiator - like battles for entertainment. If Naruto refuses, he threatens to harm the people Naruto has grown to care about in this new world.
It could be some of the traditional power - hungry ninja clans who oppose Naruto's new world order. They might see his attempts at global control as a threat to their own interests and try to undermine him.
A group of power - hungry warlords could be the main antagonists. These warlords might have emerged during the post - war period in the parallel world. They see the chaos as an opportunity to seize control over various regions. They don't care about the traditional ninja village system and are willing to use any means, including dark jutsu and enslaving other ninjas, to achieve their goals. Naruto would have to stand up against them to protect the freedom and peace of the ninja world.
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.
In a world where Naruto is a fish out of water, the local bullies or those who uphold the unfair traditions of the world could be the antagonists. They might oppose Naruto when he tries to change things for the better.
It could be a group of radical female ninjas who see Naruto as a threat to their new - found power structure. They may want to get rid of him to ensure that the world remains under their complete control.
It could be some of the old - school ninja clans who are against the new order Naruto and Hinata are trying to establish. They might see their rule as a threat to their traditional power and influence.
There could be a demonic entity in the new world. It might be awakened by Gilgamesh's arrival. This entity is used to having its way in the world and sees Gilgamesh as a new obstacle. It could possess other beings to attack Gilgamesh and use the chaos of the new world to its advantage.
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.