There could be a mysterious figure from Naruino's past during the war. This person has a grudge against Naruino and resurfaces in the post - war period to seek revenge, creating all sorts of problems for Naruino.
Another option for antagonists could be a new organization that rises in the power vacuum left after the war. They might have different ideologies from Naruino and his village. For example, they could believe in total domination rather than the peace and co - existence that Naruino stands for. They would see Naruino as a threat to their plans and try to eliminate him.
It could be about Naruino rebuilding his life. Maybe he starts a new business in the post - war era, using his skills to contribute to the reconstruction of the village.
One possible plot could be that Naruino, having survived the war, now focuses on rebuilding his village. He uses his unique skills and experiences from the war to improve the village's defenses and also to teach the younger generation how to protect themselves. For example, he could set up a training academy where he imparts his combat knowledge and ninja techniques.
It could be a rogue ninja who was once part of a minor group during the war but has now risen to power. Maybe they felt overlooked or mistreated during the war and now seek revenge on the major villages.
It could be a rogue vampire who didn't like the way the war ended and blames Alucard and Seras. This vampire might have his own ideas about how the vampire world should be ruled and sees them as obstacles.
A rogue ninja from a formerly warring village could be the main antagonist. This ninja might hold a grudge against the new peace and wants to disrupt it. He could be powerful and have his own group of followers who are also discontent with the current situation.
A new supervillain could emerge. Maybe a scientist who got access to some of the leftover technology from the Civil War battles and uses it to create a powerful weapon. He then targets Spiderman because he represents the superhero community.
It could be a power - hungry shinobi from another village. This shinobi sees Naruto's exile as an opportunity to gain more power and influence in the ninja world. He might try to hunt Naruto down to prove his own strength or to steal Naruto's secrets.
Perhaps a secret organization within the Hidden Leaf that wants to take over the village. They use Naruto as a scapegoat, getting him banished so they can carry out their evil plans without interference from Naruto. They would be the main antagonists as they are the ones behind the false accusations and the push for his banishment.
Perhaps a new, unknown force. With Naruto gone, a previously hidden group with a vendetta against the ninja villages could emerge. They might blame the villages for the destruction caused during the war and see Naruto's death as the perfect time to strike, when the villages are still recovering and vulnerable.