The shinobi council could be antagonists. They would be very suspicious of Naruto being adopted by Jenova, fearing that he will bring destruction to the village. They might try to isolate or even eliminate Naruto.
Jenova herself could potentially be an antagonist in a sense. If her motives for adopting Naruto are self - serving and harmful to the ninja world or Naruto's friends, Naruto might have to turn against her. Even though she adopted him, her actions could put her at odds with Naruto's values, making her an adversary in the long run.
Perhaps in this fanfiction, Jenova's influence causes Naruto to view his village and the shinobi world in a different light. He could start to question the long - held traditions and hierarchies. And as he is adopted by Jenova, he might have to deal with the enmity that the shinobi world has towards anything related to Jenova, thinking he is a threat.
Perhaps the main antagonists would be the dark forces in the universe that are threatened by the growing power of the Loki - Naruto duo. These could be powerful sorcerers or ancient evils. Or, it could be Loki's own family members who oppose his newfound relationship with Naruto, seeing it as a distraction from his duties in Asgard.
It could be that Kaguya Otsutsuki resurfaces in this fanfiction. Since Naruto is now under Sesshomaru's wing and growing in power, she sees him as a threat to her plans of ruling over all worlds. And from Sesshomaru's side of the story, there might be a powerful demon lord who doesn't like Sesshomaru taking in a human - like Naruto and decides to oppose them both.
Voldemort or his followers could still be antagonists. They might not like the idea of Harry being under Euryale's protection as it could make him more powerful. Another possibility could be some creatures from Euryale's world who are against her taking in an outsider like Harry.
It could be some jealous rivals of Arcuid. They might see Harry as an outsider and a threat, especially if they think Arcuid is giving Harry special treatment or powers. Maybe there are those who want to use Harry against Arcuid for their own gain.
The Joker could be a main antagonist. He would be fascinated by Harry's magic and would try to use it for his own evil purposes or just to cause chaos. He might try to drive a wedge between Harry and Batman by using mind games.
Well, Naruto is the key character as he is the one who frees Jenova. Jenova herself is a central character in this fanfiction concept. Other characters from the Naruto universe could also play roles. For example, Sakura might be concerned about Naruto's actions and try to talk some sense into him. Also, there could be some original characters created for this fanfiction. Maybe a wise old hermit in the realm where Jenova was imprisoned who warns Naruto about the consequences of freeing her, but Naruto, being stubborn, doesn't listen at first.
Another possibility is that some of the more power - hungry ninja from Naruto's own world might become antagonists. They could be jealous of Naruto's new connection with Ryu Hayabusa and the potential power and knowledge he could gain from it. These ninja might try to undermine Naruto or even try to harm Ryu to prevent Naruto from getting stronger. Maybe some of the rogue ninja or the hidden enemies within the ninja villages would see this as an opportunity to make a move against Naruto.
One possible main antagonist could be Voldemort still. Even though Harry is now under Sparda's protection, Voldemort would see Harry as a threat and would try to get rid of him. Another could be some of the demons from Sparda's world who see Harry as an intruder or a threat to their plans in the new world order that Sparda is trying to create with Harry by his side.
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.