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, 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.
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 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.
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.
It could be Sam and Tucker. Since Danny has become a villain, his former friends would likely try to stop him. They would be the main antagonists from Danny's point of view now. They would use their knowledge of Danny and their own skills to try and bring him back to the good side.
The main antagonist could be a powerful ghost who has a vendetta against Danny. Maybe it's a ghost that Danny defeated before, but who has come back stronger and is now seeking revenge. This ghost could hunt Danny down as he runs away, causing all sorts of trouble for him.