The Death Eaters could be likely villains. They are known for their cruel and dark ways in the Harry Potter universe. They might target Hermione because of her association with Harry Potter, who is their sworn enemy. They could see torturing Hermione as a way to get to Harry or to send a message to the Order of the Phoenix.
It could be a jealous classmate. Maybe someone who's always in Hermione's shadow, like a fellow Gryffindor who wants more attention. They could frame her to get her out of the way. Also, there's a chance that a Death Eater sympathizer in the school could frame her as part of a larger plot to disrupt the order in Hogwarts.
Hermione herself could be more vigilant. If she noticed any signs of danger or people acting strangely around her, she could take precautions. She could use her own intelligence and magic to create defenses. For instance, she could set up a spell that alerts her when someone with malicious intent is near, and then she could either escape or fight back.
Some dark wizards or witches who oppose the new order at Hogwarts after the fall of Voldemort could also be the villains. They might see Hermione as a threat to their plans of taking over or causing chaos in the wizarding world. They could force her to do things against her will in order to gain an advantage over the good side.
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.
Perhaps they are exploring darker themes just for the sake of exploring. However, this is a wrong approach especially in the context of the Harry Potter series. The series is mainly about hope and heroism. By writing such fanfiction about Hermione being tortured in relation to the Weasleys, they are going against the very core of what the series represents. They might not fully understand or respect the original characters and their significance.
There could be a group within the Ministry of Magic itself that is corrupt. They might not like Hermione's progressive ideas about the treatment of house - elves and other non - human magical creatures. So they conspire to put her in Azkaban to silence her and maintain the status quo.
One likely villain could be Loki. He's always up to no good and loves to play mind games, so a card game would be right up his alley. He might be the one who lures Tony into the game.
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.
Maybe a jealous wizard or witch within the Ministry of Magic. They might be envious of Hermione's popularity and influence among the younger wizards. So they fabricate evidence against her to get her locked up in Azkaban.