Sometimes, it could be characters who have been corrupted. Maybe a former ally who has turned against Percy due to some outside influence. This could add an interesting layer of betrayal to the story. The reasons for their corruption could range from being influenced by dark magic to being manipulated by a more powerful evil force.
It could be the traditional villains from the original story. Maybe some of the old enemies of Percy who have a vendetta against him. For example, the Titans or some rogue demigods who oppose him for power or personal reasons.
There might be new characters created specifically for the fanfiction. They could be powerful and cruel beings from some hidden part of the fictional world. These antagonists could be motivated by jealousy towards Percy's status or abilities. They see torturing him as a way to assert their own dominance or to gain something from him, like his powers or secrets.
It could be the traditional villains from the original story, like the Titans or some powerful monsters. They might torture Percy to get information or just to cause chaos.
Another option is a group of demons who have a vendetta against Clary or the shadowhunters in general. They might use torture as a way to break her spirit and gain information about the shadowhunters' defenses.
Even old enemies of the demigod world, who see Percy and Jason as threats, could be the antagonists. They might use deception and betrayal as a way to weaken the demigod forces, knowing that Percy and Jason are important figures among them.
There might be some new characters introduced in the fanfiction who have different ideals or motives that clash with Annabeth's. These new characters could be the antagonists as they oppose Annabeth, and Percy has to step in. For example, if they think Annabeth's way of handling a certain quest is wrong and Percy believes in her, he'll fight against their ideas.
The Akatsuki could be likely antagonists. They are always interested in powerful ninja like Naruto. They might use some forbidden jutsu to control Naruto to further their goals of collecting the tailed beasts. Another possibility is Orochimaru. He is always looking for ways to gain power and Naruto's power would be very appealing. He could try to control Naruto to use him in his experiments or to fight his enemies for him.
One likely antagonist could be a powerful new villain who has the ability to mind - control. This villain might target Deku specifically because of his potential as a hero. Another could be an old enemy of the hero society who sees Deku as a key to their revenge.
Obviously, Percy is one of the main characters as he is the one being tortured. The hunters as a group are also main characters. Among the hunters, there might be a leader or a few individuals who are more prominent in the act of torturing Percy. There could also be some of Percy's friends or allies who might try to rescue him, like Annabeth. They could be secondary characters who play important roles in the plot.
In many of these fanfictions, the demons are the main antagonists. They are the ones who carry out the torture on Sam. They might have different motives, like revenge for Sam's past actions against them or simply following Lucifer's orders.
Percy might endure it through his own stubborn will. He's a demigod used to facing tough situations. In this fanfiction, he could be using his past experiences of fighting monsters and surviving hardships. He might tell himself that he's been through worse and this is just another trial he has to pass. So he grits his teeth and bears it as best he can, even when the torture in Tartarus is beyond what he's ever faced before.