There could be a powerful and corrupt business tycoon who wants to use Naruto's powers for his own gain. He hires a team of mercenaries with some knowledge of the ninja arts to capture Naruto. This tycoon plans to use Naruto to create an army of super - soldiers or something equally evil, and Naruto has to fight against this threat to both himself and the city.
It could be a group of powerful mafia bosses who see Naruto's ninja abilities as a threat to their illegal operations. They might try to hunt him down and eliminate him before he can expose their secrets or interfere with their business.
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.
The Akatsuki remnants could still pose a threat. Members like Sasori or Deidara might have had backup plans or followers who now want revenge for the Akatsuki's downfall. They could target Naruto specifically, seeing him as the one who brought down Pain and disrupted their plans.
It could be the old enemies who see Naruto's new form or role as a threat. Maybe Orochimaru, who is always after power, would try to stop Naruto or take advantage of his new state. He might think Naruto's power in this apocalyptic scenario can be harnessed for his own evil purposes.
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 the traditional enemies from Naruto's world, like the Akatsuki. They might see the union of Naruto and Rias and their unborn child as a threat to their plans for world domination. They could try to kidnap Rias to use her as a bargaining chip against Naruto or to study the unique nature of their child.
The village elders could be antagonists. They might see Naruto as a threat due to his devil - like origin and try to eliminate him. They fear that his powers could bring chaos to the village.
One likely main antagonist could be a powerful demon lord who is trying to break through the barriers between the spirit world and the human world. This demon lord would be a major threat to Naruto and his harem, and they would have to use all their combined skills to stop it.
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.