The main antagonist could be an ancient evil spirit that has possessed the kitsune assassin. This spirit forces the assassin to do its bidding, which includes targeting Naruto. The spirit has a long - standing grudge against the ninja world and sees Naruto as a threat to its plans of domination. Naruto would then have to not only deal with the assassin's attacks but also find a way to exorcise the evil spirit from the kitsune.
It could be another powerful kitsune who wants to use the assassin for their own evil plans. This other kitsune might be jealous of the assassin's skills and wants to control them.
Maybe another kitsune who has gone bad. In the fanfiction world, there could be a rogue kitsune who sees Naruto as a threat. This antagonist kitsune might be jealous of Naruto's power or his connection to the human world. They could try to undermine Naruto's attempts to protect the village or his friends.
It could be an evil shinobi who wants to capture the Kitsune Anbu for their unique powers. Maybe they want to use those powers to take over the Hidden Leaf Village. Another option is a rogue Anbu member who has turned against the village and sees the Kitsune Anbu as a threat to their own plans.
It could be the leader of the group that the assassin belongs to. They might be using the assassin for their own dark purposes and be the main force behind any evil plans.
A powerful dark sorcerer could be the main antagonist. He might be seeking to use Percy's skills for his own evil purposes, and when Percy refuses, he becomes the target. The sorcerer would have a vast array of dark magic at his disposal, making him a formidable foe.
An ancient and forgotten god who has been awakened. This god could be angry at the modern demigods for ignoring the old ways and decides to send assassins after Percy as a warning to the rest. They might want to bring back the old order where gods were feared and worshiped more and see Percy as a symbol of the new, more independent demigods.
Obviously, Naruto would be one of the main characters. He's the protagonist of the Naruto series and would be the main link to the ninja world in this crossover. Another could be a young Kitsune, maybe one that's just coming of age in the Kitsune world. Their paths cross, and they have to learn to work together.
A new, original character could be created as the antagonist. Maybe a powerful and vengeful assassin who has a grudge against Robin for some past event. This character could have unique abilities and a personal vendetta that drives the conflict in the fanfiction.
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.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.
It could be a bully in the village. This bully could constantly pick on Naruto because of his status as the Jinchuriki of the Nine - Tails. He might try to steal Naruto's food or prevent him from playing with other kids.