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.
There could be an ancient evil entity that has been awakened by the birth of the baby. The baby's unique magic has some sort of connection to this entity's past or its plans for the future. So it becomes the main antagonist, trying to either corrupt the baby or use its power to fulfill its own dark desires.
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.
Some fanfictions feature ancient evils that were sealed away long ago but are now starting to break free. These could be powerful demons or corrupted spirits. They see Lucy and Natsu as threats to their plans of world domination, so they target them. The antagonists in these cases are not only physically powerful but also very cunning, constantly devising new ways to outwit our heroes.
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.
Rittenhouse could be antagonists. They might see the baby as a tool or a threat to their plans for controlling time. They could try to kidnap the baby to use its potential powers for their own evil purposes.
The antagonists could be dark guild members. They might hear about the special baby that Lucy and Laxus are involved with. Maybe the baby has some sort of powerful magic within it, and the dark guild wants to steal the baby for their own evil purposes. So they constantly try to attack Lucy and Laxus to get their hands on the baby.
Well, perhaps the story could start with Lucy finding out she's pregnant. Natsu is initially shocked but then becomes super excited. The pregnancy is filled with little adventures, like Natsu trying to build a perfect nursery using his magic in a rather clumsy way. And when the baby is born, it brings a new sense of hope and family to the whole guild. Everyone pitches in to take care of the baby, and it grows up surrounded by love and magic.
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.
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.
Lex Luthor could be a main antagonist. He might see the baby as a threat or a way to get to Clark. He could try to kidnap the baby to blackmail Clark into doing his bidding.