A group of power - hungry shinobi from a hidden village could be the main antagonists. They see the 'angel of darkness' as a weapon that they can use to gain supremacy over other villages. They start a series of attacks and schemes to capture the angel, putting Naruto and his allies in a difficult position as they try to protect it and keep the peace in the ninja world.
It could be the Hidden Leaf Village itself. If the village turns against Naruto through false accusations or unjust treatment, it becomes the force that drives him to the dark side. The elders or some of the more conservative ninja in the village who oppose Naruto's unorthodox ways could be the face of this antagonism.
It could be an ancient evil that has been lurking in the shadows for ages. Maybe a dark spirit that was sealed away long ago and is now breaking free, and Naruto has to control the darkness within himself to fight it.
It could be an old ninja who was once banished from Konoha for using dark jutsu and now wants revenge. He might see Naruto as a symbol of the village he hates and tries to corrupt him by luring him into the darkness.
It could be Orochimaru. He has always been interested in power and has no qualms about using dark methods. He might see Naruto as a perfect vessel or a tool to further his own dark plans, and through his manipulations, Naruto starts to be consumed by darkness.
A powerful dark spirit might be the main antagonist. This spirit could sense Naruto's new ability to control darkness and see him as a threat. So it starts causing chaos in the ninja world, forcing Naruto to use his dark - controlling powers to stop it. The spirit could have the ability to possess other ninjas, making them do its bidding.
A rogue slayer could be the main antagonist. Maybe she has gone bad and believes that Connor, being part - demon, is a threat that needs to be eliminated. She could be very skilled and use her slayer powers to injure Connor, leading to a conflict between her and those who protect Connor.
It could be a rogue ninja from within Konoha who has embraced the 'darkness' fully and wants to reshape the village according to his own twisted ideals.
A powerful sorcerer who wants to control the power of the fairy of darkness for his own evil purposes could be a great antagonist. He might try to trap her and force her to do his bidding.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.