Perhaps some new, original antagonists created specifically for the fanfiction. Maybe a group of dark mages who see Percy as a threat to their plans and decide to torture him to stop him. They could have motives related to power or control over a certain realm.
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.
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.
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.
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.
The Akatsuki could also be antagonists in an Iruka kidnapped fanfiction. They might believe that Iruka has some information about the jinchuriki, especially since he is close to Naruto. Or there could be a new, made - up antagonist in the fanfiction, like a powerful dark wizard who has set his sights on Iruka for some unknown but sinister reason. This new antagonist could add a fresh and unique element to the story.
In Kidnaped Izuku Fanfiction, likely antagonists could be rival villains who see Izuku as a threat to their plans. For example, those who want to stop him from becoming a great hero. It could also be villains who are after his unique quirk. Maybe they want to study it or use it for their own evil purposes. Another possibility is that it could be a group with a vendetta against the hero school he attends, and they target Izuku to send a message.
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.
Perhaps some rogue ninja from other villages. They might see Naruto as a symbol of Konoha's power and want to take him down to weaken Konoha. These rogue ninjas could be led by a powerful and vengeful shinobi who has a grudge against Konoha. So when Naruto is alone on a mission or something, they attack, and that's when Minato steps in to save him.
Maybe some new rogue ninja group that has a vendetta against the Uzumaki family. They see Boruto as a way to strike at Naruto, so they try to harm him, which then leads to Naruto having to save him.
One likely antagonist could be Chazz Princeton. He's often shown as a bit of a bully in the Yugioh series, and he might target Syrus out of jealousy or just to assert his dominance. Another could be an original character created by the fanfiction writer, perhaps a new student at Duel Academy who has a vendetta against Syrus for some reason. The Society of Light could also be antagonists in a sense, as they might try to manipulate Syrus or use him in their schemes, which could lead to him getting hurt.