In some cases, it could be an ancient evil that has been awakened by the meeting of Lucy and Acnologia. This evil entity wants to destroy the world and sees their union as a sign that it's time to start its plan. So it becomes the main antagonist, trying to stop Lucy and Acnologia from becoming allies and using their combined strength against it.
Maybe there's a group of dragon hunters. They view Acnologia as the ultimate prize and would do anything to capture him. When they see Lucy interacting with Acnologia, they consider her a traitor to humanity and try to take them both down. They could be the main antagonists as they constantly pose a threat to Lucy and Acnologia's new - found relationship.
It's possible that in this fanfiction, Lucy and Acnologia meet in a neutral territory. Lucy, with her kind heart, tries to communicate with Acnologia. Acnologia, who has been alone for a long time, is initially hostile. But as Lucy persists, she manages to break through his tough exterior. They might then share stories about their pasts, with Lucy talking about her guild and Acnologia about his past as a dragon.
Laxus could be seen as the main antagonist in this scenario since he is the one who kidnaps Lucy. However, it could turn out that there is a greater force behind his actions, in which case that unknown entity would be the true antagonist.
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.
Lucy could be an ordinary girl who stumbles upon the dragon by accident. Maybe she was just exploring an old forest or a mysterious cave when she came across it.
A possible main antagonist could be Aizen from 'Bleach' who somehow gains the ability to control the powers from Lucy's world as well. He could use this newfound power to try and take over both the Bleach universe and Lucy's world. His cunning and powerful abilities would make him a formidable foe for Lucy and the Bleach characters to face.
A time - traveling bounty hunter could be the main antagonist. He might be after Lucy because she has somehow disrupted the time - space continuum. He's cold - hearted and will stop at nothing to bring her to some time - traveling justice.
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.
It could be another powerful celestial dragon who opposes Lucy's ideas or presence.
Perhaps Kaguya Otsutsuki is resurrected again, but this time with a stronger will and more dangerous plans. Since Naruto was the one who played a major role in defeating her before, she targets him first in this fanfiction.
Well, clearly Lucy and Natsu are the main characters. Lucy is often depicted as a smart and resourceful character, while Natsu is more of the impulsive and strong - willed one.