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's possible that the main character is not even human. Maybe it's a spirit associated with the sakura tree itself. And then there could be other characters like a villain who tries to keep the world in darkness and those who oppose the villain, all intertwined in the story of 'sakura out of the darkness fanfiction'.
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.
It could be a new dark wizard that we haven't seen in the original series. This wizard could be extremely powerful and manipulative, and his main goal is to corrupt Harry. He might be using Harry's fame and his insecurities to draw him into the darkness.
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.
In this fanfiction, the main antagonist could be a strict teacher. Sakura, being a boy with a free - spirited nature, often clashes with the teacher's rigid rules. The teacher always seems to be out to get Sakura, giving him unfair punishments and trying to suppress his creativity or individuality.
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.