It could be someone from Natsu's past. Maybe an old rival who knows about his dark secrets and wants to use them against him.
There's a possibility that the main antagonist is an entity related to the source of Natsu's dark past. For instance, if his dark past involves a dark magic experiment, the person who conducted the experiment or a creation of that experiment could be the antagonist. They might want to either continue their experiments on Natsu or prevent him from revealing the truth about what happened.
The 'natsu dark past secret fanfiction' might revolve around Natsu's family. There could be some dark secrets about his family that he has just discovered. Maybe his family was involved in some sort of dark magic or a feud with another powerful group, and Natsu is now starting to uncover the truth about it.
It could be a dark wizard who wants to use Natsu's connection to the Dragonoid for his own evil purposes. This wizard might have set the trap to either steal Natsu's power or to use him as a sacrifice to gain more power related to the Dragonoid.
It could be an old and powerful vampire lord who sees Natsu as a threat to his rule. Since Natsu is a new and different kind of vampire, the lord might want to eliminate him.
It could be a long - lost relative of an old enemy. For example, if there was a powerful dark wizard that Natsu defeated in the past, this relative might come seeking revenge and be powerful enough to kill Natsu.
Maybe an ancient dragon that has been awakened from its slumber and views Natsu as an intruder in the dragon world. Since Natsu is a new - made dragon, this old dragon might try to drive him out or even harm him.
It could be another dark mage who sees the potential in baby Natsu and wants to use him for evil purposes. This mage might view Zeref as an obstacle in getting to Natsu.
Maybe there's a dark wizard who has a vendetta against Natsu's family. When he finds out that Natsu is secretly a girl, he sees it as an opportunity to further his evil plans. He could try to kidnap her or use her as a bargaining chip against her family or friends. He might think that because she's a girl, she'll be easier to manipulate or capture compared to if she was thought to be male.
It could be a dark wizard who wants to use the baby's power for his own evil deeds. Maybe the baby has some special magic that the wizard thinks can help him take over the magical world.
His friends could be involved. For example, Lucy might stumble upon some old records or meet someone who knew Natsu in the past. Gray could also be part of it, especially if it has something to do with the magic world's secrets that they both are a part of.
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.