Perhaps there are other slayers who have turned bad and are now competing with Lucy. They might want to be the only one with the title of 'fairy slayer' and see Lucy as an obstacle in their path.
It could be powerful fairies who have a vendetta against Lucy for being a slayer. Maybe they are the leaders of a fairy clan who see her as a threat to their existence.
It could be a group of students from another academy who are jealous of Fairy Tail Academy's reputation. They constantly try to undermine Natsu and Lucy's efforts and cause trouble during competitions.
It could be another guild that sees Natsu as a threat. They might find out about Lucy kidnapping Natsu and try to use the situation to their advantage. For example, they could try to steal Natsu's magic or get information out of him while he's in a vulnerable state. Another possible antagonist could be a character who has a grudge against Lucy. They might try to stop her from getting away with the kidnapping or use it as a way to get revenge on her.
A group of dark fairies could be the main antagonists. They might be jealous of Natsu's power or his unique status as a fairy and try to undermine him at every turn.
It could be a group of jealous students who don't like Natsu and Lucy being in charge. They might try to undermine their leadership by causing trouble during important events at the academy.
It could be a rogue Dragon Slayer who is jealous of Lucy's new - found powers. This character might have been exiled from their own guild for misusing their powers and now sees Lucy as an easy target to prove their superiority.
In this fanfiction, a main antagonist could be a powerful dark witch who has the ability to summon and control hordes of monsters. She believes that the wizarding world has become too soft and that only through chaos and fear brought by the monsters can it be purified. Harry, as the Monster Slayer, is her biggest obstacle. Another antagonist could be a group of Death Eaters who have discovered a way to use monsters as weapons in the post - Voldemort era. They want to continue the dark legacy and see Harry as the one who will always stand in their way. Also, a mysterious figure from the past, a forgotten dark wizard who has been locked away for centuries but is now free and is using monsters to exact his revenge on the modern wizarding world.
It could be an organization of rogue ninja who have also somehow gained similar powers but use them for destruction. They see Naruto as a threat to their plans of taking over the ninja world with their newfound powers. They constantly try to undermine Naruto and steal his unique Crystal Dragon Slayer techniques.
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.
Maybe a rival guild that is jealous of Fairy Tail's new addition. They might think that having a baby with such strong magical potential in Fairy Tail gives them an unfair advantage. So they try to kidnap the baby to either keep it for themselves or use it to bargain with Fairy Tail.
Well, if we consider Lucy as a Dragon Slayer in fanfiction, her magic could be really different from the traditional ones. Maybe she'd have a connection to a celestial dragon, which would be so cool. It would combine her existing celestial spirit magic with the new dragon slayer powers. She could use the stars as a source of power, similar to how other dragon slayers use elements, and it would be a fresh take on her character.