Vlad could be a great antagonist. He might see the baby versions of Danny and Sam as an opportunity to finally get rid of Danny for good. He could try to use their weakened state to his advantage and steal Danny's powers once and for all.
A new ghostly entity could be the main antagonist. This entity might be attracted to the chaos caused by Danny and Sam being turned into babies. It feeds off the confusion and tries to spread more disorder in Amity Park while targeting the defenseless baby Danny and Sam.
Well, it could be that there is no traditional antagonist. Sam's betrayal could be the main source of conflict, and she could be seen as the antagonist in Danny's eyes for that time being. But if there has to be another force, it could be the entity that influenced Sam to betray Danny in the first place. For example, a powerful and manipulative ghost that has its own agenda and uses Sam as a pawn.
A group of human hunters who have decided to target Danny's ghost side could be the antagonists. They might be trying to capture Danny and use him for their own experiments. Danny, feeling violated and angry, decides to take revenge by using his ghost powers to outwit them at every turn, and expose their cruel intentions to the people of Amity Park.
It could be Vlad Masters. Since he's always been interested in Danny's half - ghost state, he might see Sam becoming a half - ghost as an opportunity to gain more power or to use her against Danny. He could try to manipulate her new powers for his own evil plans.
Well, it would be the evil Danny Phantom. Consider this: he has gone through some transformation that has made him evil. Now he is using plants in ways that are harmful or against the natural order. Sam, who has a connection to plants and a moral compass, is in direct opposition to him. He creates the conflict in the story by his evil deeds, and Sam has to find a way to overcome his actions, so he is the main antagonist.
A new and powerful ghost that Danny has never faced before could be the main antagonist. This ghost could have unique powers that Danny isn't prepared for, and in their first encounter, it manages to defeat and kill Danny. This would set the stage for a story of revenge or trying to bring Danny back.
In the 'danny phantom is a lion fanfiction', the main antagonist could be a group of anti - phantom scientists who capture Danny when he's in lion form. They want to study his unique physiology and use his powers for their own evil experiments. They see him as a threat to their control over the human - ghost interactions and will stop at nothing to keep him locked up and experiment on him.
A new, powerful ghost that hates the Christmas cheer could be the main antagonist. This ghost could be spreading gloom and trying to cancel Christmas in Amity Park. Danny would have to figure out the ghost's motives and stop it from ruining everyone's Christmas. For example, it might be a ghost who was once a Scrooge - like figure in life and now wants to make others as miserable as he was.
One possible plot could be that Danny and Sam face challenges in raising their baby while also dealing with Danny's ghost - fighting duties. Maybe the baby inherits some of Danny's powers and they have to figure out how to help the baby control them.
The Guys in White could be the main antagonists. If Danny becomes evil, they might see this as their chance to finally capture and experiment on him. They would be constantly chasing him, which would make Danny see them as the main obstacle in his new evil plans, and thus they would be the antagonists in the story.
A powerful ghost that has taken over the Circus Gothica and is using it to draw in innocent souls. This ghost might have a vendetta against Danny specifically or just be generally evil and want to spread chaos.