Perhaps an ancient evil spirit that has a connection to death itself. This spirit sees Naruto as a threat because of his emerging powers related to death and tries to eliminate him before he becomes too powerful. The spirit could be using other villains as pawns to do its bidding.
One potential main antagonist could be Orochimaru. Since he is always interested in immortality and forbidden jutsu, he would surely be intrigued by Naruto's condition. He might try to capture Naruto to conduct experiments on him to gain the secret of his immortality for himself.
Another option is a dark cult that worships chaos. They believe that the dragon child's destiny to bring balance will disrupt their plans for a world in anarchy. So, they set out to corrupt the dragon child or kill it to keep their vision of chaos alive.
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 Titans could be great antagonists. They might see Percy as a threat to their plans of overthrowing the gods again. Since Percy has chaos powers, they could fear that he could disrupt their carefully laid - out schemes. Another possibility is some of the more traditional enemies of the demigods, like the monsters. They might be drawn to Percy's chaotic energy and try to either consume it or destroy him to prevent him from becoming too powerful.
Maybe it's a group of intergalactic criminals who are after the power that Peter Parker has as a 'child of the universe'. They could be stealing artifacts from different planets to gain more power and they see Peter as the ultimate source of power that they need to complete their collection.
Another potential main antagonist could be a force from Harry's world that has followed him into the Kuroshitsuji crossover. This could be some sort of entity that doesn't want Harry interfering with the natural order of the Kuroshitsuji universe. It could be a being that has its own motives for keeping death and the afterlife in a certain state and sees Harry's actions as a threat, and so it actively tries to stop him.
Another antagonist could be a group within the ninja village itself. Maybe they fear the changes that the child of prophecy might bring. They could be the more conservative elements who don't want to see new ideas or powers emerging. They might try to undermine the child's training or spread false rumors about them. For example, they could claim that the child is a danger to the village, turning public opinion against the child.
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.