It could be the previous Dark One who doesn't want to give up their power completely. Even though Emma has become the new Dark One, the old one might try to manipulate her from the shadows, trying to get her to make mistakes that would allow them to regain their power.
The main antagonist could also be the darkness itself. Since Emma has become the Dark One, the very essence of the dark magic within her could be trying to overtake her completely. It would be like an internal struggle, but personified as an antagonist. The darkness could be constantly whispering in her ear, urging her to do evil deeds, and she has to resist it in order to keep her sanity and not become a true villain.
Perhaps it's one of Percy's former friends who has turned against him. This friend could be jealous of Percy's powers or has been influenced by some dark force. Their actions and taunts could be what drives Percy to become dark, making them the main antagonist in the story.
Well, one possible plot could be that Emma, after being pushed to her limits by the constant threats in her world, decides to embrace the power of the Dark One. She might start off using it for what she believes is the greater good, like protecting her loved ones from a new, more powerful enemy. But as she delves deeper into the dark magic, she starts to lose herself. Her relationships begin to fray as her friends and family see the changes in her. And she has to struggle with the internal battle between her old self and the new, dark self that is emerging.
It could also be a new character, perhaps a dark sorcerer who is jealous of the magic in Neverland. This sorcerer might target Emma because she has an unknown power within her that could disrupt his own plans for the magical world. He would try to separate her from Peter Pan and use her power for his own evil deeds.
The Evil Queen could be a great antagonist. She might see the relationship between Emma and Rumpelstiltskin as a threat to her power. She could try to drive them apart by creating misunderstandings and false scenarios that make them doubt each other.
Perhaps a group of dark side cultists could be the main antagonists. They idolize the power of the dark side and see Ahsoka as a prime candidate to join their ranks. When she refuses at first, they start to hunt her down, but in the process, they unknowingly push her closer to the dark side, creating a complex dynamic where they are both the pursuers and the inadvertent cause of her fall to the dark side.
The Green Goblin could be a great main antagonist in a dark fanfiction. He could be even more deranged and have a more elaborate plan to destroy Spider - Man, not just physically but also mentally by targeting his relationships.
The World Government could become the main antagonist. They would see Luffy's new power as a threat, especially if he starts using it in ways that oppose their rule. They might send out their strongest agents, like the Admirals, to take Luffy down. The Admirals could have developed new techniques to deal with the dark dark fruit powers, making them a formidable foe for Luffy.
There could also be new antagonists. For example, some of the more traditional wizarding families who are against the idea of a female Harry. They might see her as a threat to the old - fashioned ways of the wizarding world and try to undermine her.
Perhaps it's a jealous ninja from another village. This ninja has always been envious of Naruto's power. So when he gets the chance, he uses a dark magic to turn Naruto into a wolf. His goal is to make Naruto weak and lose his status among the ninja community.
The main antagonist could be an evil knight who has a vendetta against dragons. When the princess turns into a dragon, he sees her as a prime target and tries to slay her, believing all dragons are evil. He doesn't care that the princess was once human and is only focused on his own prejudiced views.