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.
One possible plotline could be Clary's friends finding out about her being tortured and launching a rescue mission. They might face many obstacles on their way to save her, like fighting off the torturers' guards.
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.
One possible plot could be that Clary gets drunk and ends up confessing her hidden feelings to someone she has a crush on.
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.
One possible antagonist could be an alien bounty hunter who wants to take the Omnitrix from Gwen for his own purposes.
In some fanfictions, Clary might get hurt because of a betrayal within the Shadowhunter community. For example, someone she trusts might lead her into a trap where she gets injured. It could be a complex plot where the betrayer has their own motives, like jealousy or a desire for power. This would not only physically harm Clary but also emotionally shatter her trust in those around her.
Well, in some fanfictions of this kind, Naruto could be tortured physically by being chained up and beaten. His captors might also starve him or deprive him of water to weaken him. It could also be that they use some sort of dark magic or forbidden techniques on him that cause extreme pain and discomfort.
Sometimes, it's just a way to shock the audience. Fanfiction authors often like to take risks and do unexpected things to their beloved characters. Torturing Natsu can be a very unexpected and extreme move that can leave a lasting impression on the readers, whether they like it or not.
In this fanfiction, perhaps Marinette endures the torture and it changes her in some way. She could become more determined to defeat Hawkmoth. After the torture, she might train harder, learn new skills, and become a more formidable opponent. She could also develop a deeper understanding of Hawkmoth's motives, which could be crucial in finally stopping him.