His ghost - hunting parents could potentially betray him. If they found out Danny was half - ghost, they might see him as a threat to humanity rather than their son. They've been so dedicated to hunting ghosts that their views could be clouded, and they might not be able to accept Danny for what he is, leading to a heartbreaking betrayal for Danny.
In a crossover, characters from the other franchise might betray Danny. For example, if it's a crossover with a show about vampires, a vampire character who seems friendly at first could betray Danny for his ghost powers. They might want to use his powers for their own dark purposes. Another likely candidate could be a character who is jealous of Danny's abilities. Maybe in a crossover with a superhero world, a sidekick who feels overshadowed by Danny's powers and popularity might be the one to betray him.
It could be Valerie. She has had a somewhat rocky relationship with Danny in the original series. In a fanfiction about betrayal, she might be pushed over the edge by jealousy or a misunderstanding about Danny's powers and his intentions. She could then use her ghost - hunting skills against Danny in a more malicious way than before.
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.
Danny would probably be extremely hurt. He might initially go into denial, not wanting to believe that his friends could do such a thing to him. He'd keep trying to reach out to them, hoping it was all a misunderstanding.
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.
He might meet a nurse who has some sort of psychic ability and can sense that Danny is different. This could lead to an interesting interaction where Danny has to be extra careful.
Sam is also quite popular. Her goth - like personality and her strong - willed nature make her an interesting character. In fanfiction, she can be portrayed in different ways, like being even more involved in Danny's ghost - fighting activities.
Perhaps Danny's friends are lured by a powerful and evil ghost who offers them something they desire, like wealth or power. In exchange, they have to turn against Danny. They might start to sabotage Danny's ghost - fighting efforts, for example, by giving false information to his enemies. This would be a huge betrayal considering they were once his closest allies.
He could be handcuffed together with his sister Jazz. It would be an interesting dynamic as they have a typical sibling relationship, and being handcuffed would force them to be in close proximity and deal with each other's quirks in a new way. Maybe they have to solve a mystery while handcuffed.
It could be Vlad Masters. He has always been jealous of Danny and his powers. Maybe he finally decides to take extreme measures and kidnaps Danny to steal his powers once and for all. He could use his advanced technology and ghost powers to keep Danny trapped.