It could be a young and innocent bystander. Maybe someone who was just in the wrong place at the wrong time. For instance, a small child who happened to be near where Will and Phobos were planning their kidnapping and was grabbed instead of their intended target.
Perhaps it's a love interest of one of the main heroes. If it's a story with a hero - villain dynamic, Will and Phobos might think that by kidnapping the hero's love interest, they can get the hero to do what they want. This would create a lot of tension and drama as the hero tries to rescue their loved one.
One possible plot could be that they kidnap a character to gain some sort of power. Maybe they think the kidnapped character has a special ability or knowledge that they need. For example, if it's in a superhero - themed fanfiction, the kidnapped character might be able to control an element, and Will and Phobos want to use that power for their own evil plans.
It could be Iris. Since she's an important character in The Flash's story. The Flash might be forced to kidnap her for some strange reason, like to protect her from a threat that he can't explain to her directly.
A young journalist who has been writing articles about Kaito Kid and his heists. Kaito Kid kidnaps the journalist to control the narrative. He wants to make sure that the journalist doesn't publish any more information that could give away his next moves or expose his secrets.
The victim could be Alec Lightwood. Since Magnus and Alec have a complex relationship, a fanfiction could explore what would happen if Magnus kidnapped Alec, perhaps out of some miscommunication or a threat to Alec's safety that Magnus thought he could only handle by taking Alec away. Another potential victim could be a young, inexperienced warlock. Magnus might kidnap the warlock to teach them about their powers in a more secluded environment away from the prying eyes of the Shadowhunters.
A young boy who is the chosen one to bring about a new era of warmth could be the victim. Jack Frost kidnaps him to prevent the change in the world's climate that would come with the boy's power.
It could be Clary. Since she is a very important figure among the Shadowhunters and has a lot of power, Magnus might kidnap her if he thought it would help him achieve a certain goal. Maybe he needs her unique rune - drawing abilities for a spell.
The victim could first go to the police. Reporting the kidnapping and the non - consensual surgery is crucial. The police can then start an investigation and gather evidence.
It could be April. Since she's a human and often involved with the Turtles' adventures, she might be an easy target. Maybe the bad guys convinced Mikey and Donnie that April was in some way endangering them.
Hermione Granger might also be a main character. Given her intelligence and thirst for knowledge, she would probably be involved in researching about Phobos and its implications in the magical world. She could be the one to figure out how to use or counter any threats related to Phobos.
It could be an old enemy of Keith's, someone from his past who has a vendetta against him. Maybe a former rival from his days in the military academy who has now turned to more devious means.