It could be a rogue Kumo ninja who is jealous of Naruto's power and wants to prove himself by defeating Naruto. This ninja might have some dark secrets and a grudge against Kumo as well.
Maybe the main antagonist is an outside force, like a group of powerful mercenaries hired to disrupt the peace between Konoha and Kumo. They target Naruto because they know he is a key figure in maintaining the alliance.
Another possibility is that there is a rogue ninja in Kumo who uses Naruto's neglected state to his advantage. He might try to manipulate Naruto into doing things that would be bad for both Naruto and Kumo, all while remaining in the shadows and making it seem like Naruto is acting on his own accord.
It could be a rogue Kumo ninja who wants to steal Naruto's seal - mastering knowledge for his own evil purposes. Maybe he wants to use the seals to take over Kumo or even the whole ninja world.
Well, one potential partner could be Omoi. I know he's male, but in some fanfictions, gender - bending or same - sex relationships are explored. Omoi's unique personality, with his over - thinking and yet loyal nature, could create an interesting relationship with Naruto. However, if we stick to the more traditional female partners, Yugito Nii could also be a great choice. She was a jinchuriki, just like Naruto, and they could share a special bond based on that shared experience.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
Well, Naruto is obviously one of the main characters. He's the central figure who brings his own skills and experiences from Konoha to Kumo. Then there would likely be some original Kumo characters created for the fanfiction. For example, a strong Kumo ninja who becomes Naruto's rival or friend. There might also be a Kumo leader or elder who plays an important role in how Naruto is received and integrated into the village.
It could be Orochimaru. He's always been interested in immortality and reanimation techniques. Maybe he reanimates Naruto for some evil purpose, like using Naruto's power to take over the ninja world.
Maybe it's a ninja who has also been affected by Anodite magic but has turned to the dark side. This ninja could be jealous of Naruto's new powers and want to take them for himself. He would use his knowledge of both ninja techniques and Anodite powers to try and defeat Naruto.
It could be a rogue ninja from a rival village. This ninja has a personal vendetta against Konoha and specifically targets Team 10 because of Naruto's presence. He might be jealous of Naruto's growing power and fame and wants to prove himself by defeating the team.
There could be a group of rogue ninjas from Naruto's world who have somehow found their way to Venelana's place. They want to use the resources there for their own evil purposes and see Venelana and Naruto as obstacles in their path, thus becoming the antagonists.
It could be a dark figure from Greek mythology who wants to stop Naruto from fulfilling Apollo's will. Maybe a Titan who is jealous of Naruto's new - found connection to Apollo.