Another option could be a group of pirates who believe that the Ruby of the Sea can lead them to a great treasure. They constantly try to capture the Ruby and the Jester has to fend them off to protect her. The pirates would be a constant threat throughout the fanfic.
A jealous mermaid or sea creature who has feelings for the Ruby of the Sea could also be the antagonist. She might be envious of the relationship between the Jester and the Ruby and try to break them apart using her own charm and magic.
It could be that the Ruby of the Sea is a powerful entity and the Jester is drawn to her power. Initially, they have a bit of a rocky relationship as the Jester tries to use her power for his own gain, but over time, he realizes the importance of her as a being and they form a more sincere relationship.
It could be someone from Ruby's world who doesn't like the idea of her training an outsider like Naruto. Maybe a powerful mage or a warlord who sees Naruto as a threat to their power or the balance of their world.
It could be a powerful Grimm - like being that has evolved beyond the normal Grimm. This antagonist might have the ability to think and strategize like a human, making it a much more dangerous foe for Ruby and her team. It could be leading the Grimm attacks in a more organized way, targeting specific areas to cause maximum chaos.
Perhaps an ancient evil spirit that was sealed away long ago in Naruto's world but gets awakened by Ruby Lemon's presence. This spirit has the ability to possess people and use their skills for its own ends. It starts to cause chaos in the ninja villages and targets Ruby Lemon and Naruto specifically, seeing them as the key to either its complete destruction or its total domination.
The jester could interact with the main heroes in the League. For instance, they might have a lot of scenes with the most popular hero, constantly trying to make them laugh or annoy them. This would create a fun and engaging relationship between the two characters.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
The main antagonist could also be a new character created specifically for the fanfic. This character could be an ancient evil that has been waiting for an opportunity to corrupt a powerful Huntress like Ruby. They would then use Ruby's newfound evil nature to further their own dark plans, and Weiss, Blake, and Yang would have to face both Ruby and this new threat.
It could be Salem. She has always been interested in the power of the silver eyes, and Ruby having those eyes makes her a prime target. Salem might send her minions to kidnap Ruby, which would lead to her disappearance.
Maybe an evil sorcerer from a third, unknown dimension who sees the potential in both Naruto's chakra and Pneuma's power. He plans to steal their powers to become invincible. He starts by creating unrest in both their worlds, pitting their friends and allies against them. Naruto and Pneuma must figure out his true identity and stop him before he succeeds in his devious plan.
It could be an evil ninja who has somehow gained access to the technology from Neo's world and wants to use it to take over the Naruto world. He might be able to create clones using digital technology, making him a very difficult enemy to defeat.