One possibility is a group of shinobi from a rival village. They believe that Naruto's mother held the key to some great power or secret that could give their village an edge. So, they try to either capture Naruto to extract the information or stop him from uncovering more about his mother. Another could be a dark spirit that was somehow sealed away by Naruto's mother long ago, and now it's trying to break free and take revenge on her through Naruto.
It could also be some external enemies who see Naruto's new relationship as a weakness. They might target the mother to get to Naruto, thinking that by hurting her, they can make Naruto vulnerable. So these external forces would be antagonists trying to disrupt their relationship.
It could be Orochimaru. He has always been interested in power and the secrets of the tailed beasts. So, he might see Naruto and the Jinchuuriki family as a source of great power to experiment on or steal from.
It could be some rogue ninjas who are after Lemon for some reason. Maybe they think she has a special power that they can use for their evil plans.
One potential antagonist could be those within the village who oppose Naruto's relationships. They might see his harem as a threat to the traditional values of the village and try to cause trouble for Naruto and his partners.
It could be some hidden members of Naruto's family itself. Maybe there are relatives who have been manipulating things from the shadows and their actions led Naruto to believe he needs to take revenge on the family as a whole.
The elders of his family or clan could be the main antagonists. They might have exiled Naruto in the first place due to some old - fashioned beliefs or fear of his power. Throughout the fanfiction, they could try to stop Naruto from finding out the truth or coming back to the clan.
His family members themselves could potentially be antagonists in a sense. If Naruto is rejecting them, there could be some family members who try to stop him from leaving or try to change his mind forcefully. They might see his rejection as a threat to the family's reputation or unity.
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.