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.
Perhaps the torture is part of a scheme by an enemy to get information from Clary. She could be strong - willed and resist, and during the torture, she has flashbacks to her training and happy memories with her friends which give her strength.
It could be that the torture is a misidentification. The torturers think Clary has some important information or power that she doesn't actually have. As she endures the pain, she tries to convince them of their mistake while also looking for a way to escape.
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.
The plot could involve Clary's search for the baby's father if he's not initially involved. She might face challenges like him denying the paternity or him being in a difficult situation himself. As she tries to get him involved, she could learn more about his family and background, which could lead to unexpected twists in the story, like uncovering family secrets or feuds that now affect their situation.
In this fanfic, it might be that Fleur has been wrongly accused of a crime by a powerful magical authority. Harry tries to defend her but is captured instead. The authority tortures Harry to force him to give up on Fleur. However, Harry refuses. He endures the physical and mental pain of the torture. His perseverance might inspire some of the other characters to see the truth. Eventually, they join forces with Harry and they manage to expose the real culprit and save Fleur.
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.
One possible scenario could be that he is captured by an enemy ninja group who wants to extract information from him. They might use various cruel methods like chakra - draining techniques or physical harm. Another could be that he is tortured as a form of revenge by someone he has defeated in the past.
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.
One possible plot could be that Clary gets drunk and ends up confessing her hidden feelings to someone she has a crush on.
One possible plotline could be Clary finding out about Jace's cheating and feeling extremely betrayed. She might then decide to leave him and try to build a new life for herself and her unborn child.
In some fanfictions, Percy's torture in Tartarus could be part of a grander scheme. For example, an enemy on the surface world has made a deal with the forces of Tartarus to weaken Percy. As he endures the torture, he gradually uncovers the conspiracy and tries to find a way to not only escape but also stop those who sent him there. His friends, unaware of his situation at first, start to suspect something is wrong and embark on a quest to find out what happened to him and rescue him.