Another possibility is that an ancient evil entity that was once sealed away by Naruto's bloodline ancestors is awakened by Naruto's growing power. This entity sees Naruto as a key to either its complete freedom or its destruction, and thus becomes the main antagonist, constantly sending minions or using its own dark powers to try and stop or control Naruto.
The main antagonists could be members of an ancient clan who see Naruto's emerging powers from his bloodline as a threat to their own plans for power. They might fear that his newfound abilities will disrupt the balance of power they have been carefully cultivating for generations.
Maybe it could be other ninja clans who are jealous of Naruto's newfound sword bloodline. They might see it as a threat to their own power and status in the ninja world.
The Akatsuki might also be the main antagonists. They were after the bijuu in the original story. With Naruto having two, they would surely target him. They might see it as an opportunity to gain an even greater edge in their plan to control the world.
Some secret organizations that have been manipulating bloodline abilities for their own gain could also be the antagonists. They would not want Naruto to disrupt their plans. They might send their most powerful agents to stop Naruto, leading to intense battles in the fanfic.
One possible antagonist could be a rogue ninja who also wants the power of the Rinnegan. He might see Naruto as a target to either steal the power from or eliminate so that he can be the most powerful in the ninja world. This character could be a new creation or an existing villain with a new motivation.
It could be a rogue ninja who also has a rare bloodline and sees Naruto as a threat to his own power and status. This antagonist might want to steal Naruto's bloodline or simply eliminate him to be the only one with such a special ability.
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 old shinobi council from his former village could be antagonists. They might still see Naruto as a threat even in exile and try to harm his kids to prevent them from becoming powerful. Or perhaps some new villains who want to use Naruto's kids to get to him, knowing his strong bond with them.
Another possibility is that the antagonist could be a dark - side version of Naruto himself. The discovery of the forgotten bloodline could stir some dark desires within him. This internal struggle could be personified as a separate entity that tries to take over Naruto and use the power of the bloodline for evil. Naruto would then have to fight against this internal darkness as well as external threats who are also interested in his new - found power.