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.
Another option could be a group of fairies from a rival clan. They see the fairy of darkness as a threat to their way of life and try to eliminate her. They might use underhanded tactics like spreading false rumors about her to turn other fairies against her.
Perhaps an ancient and malevolent spirit that was sealed away long ago. The fairy of darkness accidentally releases it while exploring an old, forbidden part of the magical realm. Now, the spirit wants to use the fairy's power to regain its full strength and take over the world of fairies and beyond.
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 a powerful dark wizard who wants to use Sakura's powers for his own evil purposes. He might be constantly trying to capture her or manipulate her into doing his bidding.
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.
It could be an evil fairy king. He might see the poison fairy as a threat to his rule. Maybe he believes that her powers are too dangerous and wants to either control her or get rid of her. He could send his minions after her and try to spread false rumors about her in the fairy community.
The main antagonist could be a powerful and ancient fairy who has been banished long ago but now returns to seek revenge on the fairy world. And Lucy, being a new and important part of the fairy world, becomes a target. This antagonist might have unique and dark magic that makes it extremely difficult for Lucy to defeat. Also, the antagonist could have some sort of grudge against the fairy queen or king, and Lucy is caught in the middle of this power struggle.
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.
Another antagonist could be a human with a grudge against Danny. This person discovers Danny's 'Prince of Darkness' potential and decides to use it against him. They might team up with some lesser ghosts and use dark magic or technology to try and take Danny down. They could be motivated by jealousy or a desire for power.