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.
The Seelie Queen could be an antagonist. She might see the unborn child as a threat to her power or a valuable asset to control. So, she could try to manipulate Magnus and Clary throughout the pregnancy.
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.
Perhaps it could be a group of bullies from Issei's school days. They used to pick on him and now he's coming back to make them pay.
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.
The Dementors first and foremost. They don't really care about justice or innocence, and their actions are a form of torture. Then, there could be a new dark wizard or group that has emerged and wants to use Harry's situation to their advantage. They might have bribed the Azkaban staff or found a way to get in and torture Harry for their own purposes, like getting information about the Order of the Phoenix or just to create chaos in the wizarding world.
A third plot twist could be that the attack is a diversion. While Clary is fighting the demon, something much more significant is happening elsewhere. Maybe a powerful artifact is being stolen or a key location is being infiltrated, and by the time she realizes it, she has to race against time to stop the real danger.
One possible plot could be that Clary gets drunk and ends up confessing her hidden feelings to someone she has a crush on.