There could be a powerful organization that exists in both worlds. They see Naruto as a threat because he could disrupt their plans to rule over both universes. They have advanced technology from the Beyond Two Souls world and powerful ninja techniques from Naruto's world, making them a formidable antagonist.
Maybe a corrupted spirit from the Beyond Two Souls world that has a vendetta against Naruto for invading its territory. This spirit could use its otherworldly powers to create chaos and try to destroy Naruto and his new friends. It might be able to possess people or objects, making it a very difficult enemy to defeat.
It could be an evil ninja from Naruto's world who has somehow also gained access to the powers of the Beyond Two Souls world. This character could use these new powers to try and take over both worlds.
It could be a powerful spirit that is enraged by Naruto's soul - eating. This spirit might have been protecting the souls in the first place and now sees Naruto as a great threat.
In this fanfiction, perhaps Naruto is transported to the world of Beyond Two Souls. He discovers new chakra - like powers there. He has to learn to control these powers while also dealing with the complex characters and situations in that world. For example, he might have to figure out how to interact with the different spirits that exist in the Beyond Two Souls universe.
A great Naruto and Beyond Two Souls fanfiction could focus on the themes that both works share. Both deal with self - discovery and the power within. In a fanfic, we could see a character from Naruto, say Naruto himself, traveling to the world of Beyond Two Souls and having to come to terms with a different set of rules and powers while still holding onto his own values. It would be a journey of growth and adaptation.
One possible unusual pairing in Naruto and Beyond Two Souls fanfiction could be Sasuke and Jodie. Their personalities are so different. Sasuke is brooding and focused on revenge, while Jodie is more empathetic and in tune with the spiritual side. Their interactions could be full of tension and growth as they learn from each other.
Ink could be a great antagonist. He has the ability to manipulate his body into various weapons and forms. He could be seeking to take over Gotham's underworld in the 'Batman Beyond' era and sees Nightwing and Batman Beyond as threats to his plans.
There could be a group of anti - ninja revolutionaries as the main antagonists. They see Naruto's return with the swords as a threat to their plan of overthrowing the existing ninja order. They try to take the swords from Naruto to use them as symbols of their new regime, believing that the power of the swords will help them convince other ninjas to join their cause.
It could be Orochimaru. He's always been after power and Naruto having the power of two Bijuus would be very tempting for him. He might try to extract the Bijuus from Naruto to use for his own evil purposes.
Brother Eye could be a possible main antagonist. If it were to gain the ability to time - travel, it could try to rewrite history to create a world where it has complete control. It could manipulate events in different eras to eliminate any threats to its dominance, and Batman Beyond would have to stop it from achieving its goal.
A possible plotline could be a conflict between the two worlds. Maybe some evil force from Beyond Two Souls wants to use the power of the tailed beasts in Naruto's world, and Naruto and his friends have to stop them. Another could be a friendship - based plot where a character from Naruto, like Sasuke, befriends Jodie Holmes and they exchange knowledge about their respective worlds.
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.