It could be an evil time - traveling wizard. He's jealous of Danny's powers and wants to steal them. He uses his magic to create all sorts of obstacles for Danny and Sam as they travel through time, trying to prevent them from getting back to their own time.
A powerful alien race that has mastered time travel could be the main villain. They see Danny and Sam as threats to their plans of taking over different time periods and timelines. So they send their agents to hunt Danny and Sam down, and Danny and Sam have to outwit them while also trying to understand the aliens' motives and how to stop them.
They might have adventures like exploring ancient civilizations. Maybe they meet historical figures and learn from them. For example, they could meet Leonardo da Vinci and watch him paint. Or they could end up in a prehistoric era and see dinosaurs.
One idea could be that Danny and Sam accidentally travel back to the age of dinosaurs. They have to figure out how to survive among the giant creatures while also trying to find a way back home. Maybe they discover a time - traveling dinosaur that helps them in some way.
Danny's adventurous spirit would make him eager to jump into different time periods and experience new things. However, Sam's more reserved nature would ensure they think about the consequences first. For instance, when they come across a strange time - based phenomenon, Danny might want to rush in while Sam would want to study it more before acting.
One idea could be that Danny and Sam have kids in the future and their kids inherit Danny's ghost powers. The story could focus on how they learn to control their powers while also dealing with normal kid stuff like school and making friends. It would be interesting to see how Sam, as a mom, guides them through this.
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.
Perhaps in the fanfiction, Danny discovers that there is a threat in the past that could change the future in a very bad way. He, along with Sam and Dani, time - travels to stop it. Along the way, they meet younger versions of their friends and family. Dani starts to understand more about her family's history and her own place in it. Sam has to deal with the differences in the past's social norms compared to their time. And Danny battles villains from the past who are trying to take over the future using the knowledge of time travel they accidentally introduced.
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.
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.
Darkseid could be the main villain. Imagine Darkseid learning of Superman's ability to time - travel and using it to his advantage. He could try to invade different time periods to gain more power and resources. Superman would have to fight him across time and space to protect all of existence.
The Emperor could still be a main villain even in a Padme time travel fanfiction. If Padme travels to a time when the Emperor is already in power, he would surely oppose her as she represents a threat to his rule. He might try to manipulate events to keep her from changing the future or past, depending on where she travels to.