One idea could be that Magnus kidnaps a Shadowhunter to force them to reveal a secret that could save the Downworld. He might believe this Shadowhunter has crucial information that the Nephilim are hiding. Another could be that Magnus is being controlled by a dark force and kidnaps someone as part of its evil plan. Then, the kidnapped person's friends have to find a way to break the control on Magnus and save their friend.
In some fanfiction, Magnus might kidnap a Shadowhunter in order to trade for something he needs. For example, he might need a powerful magical artifact that the Shadowhunters possess. By kidnapping one of them, he hopes to start negotiations. This could set off a chain of events where both sides have to make difficult decisions and alliances might be formed or broken.
A fanfiction could explore the idea of a character from Twilight becoming a Shadowhunter. For example, Bella could discover she has Shadowhunter blood and has to leave the vampire - werewolf drama behind to learn a whole new set of skills and rules in the Shadowhunter world. It would be interesting to see how she adapts and how her relationships with Edward and Jacob change as a result.
Another plot could involve an OC who comes from a long - lost line of Shadowhunters. They bring back an ancient fighting style or a forgotten weapon. This OC could be on a quest to rediscover their family's past and in the process, they end up uncovering secrets about the Shadowhunter world that could change everything. Maybe they find a hidden lair with powerful artifacts that were thought to be lost forever.
One plot idea could be that Snape kidnaps a student he suspects of being involved in a dark magic plot against Hogwarts. He wants to question the student privately to get to the bottom of it. Another could be that he kidnaps someone he believes has information about Voldemort's next move, thinking he can protect that person and extract the information at the same time. Or perhaps he kidnaps a character in a fit of jealousy or to protect them from a greater danger he foresees.
One idea could be a crossover where the characters from both universes team up to fight a common supernatural threat that is a combination of demons from Supernatural and Downworlders from Shadowhunters. For example, a powerful demon has made a pact with a group of rogue vampires to take over both the human world and the Shadow World.
A plot could involve a Twilight vampire falling in love with a shadowhunter. The vampire has to deal with the shadowhunter world's rules about the supernatural, and the shadowhunter has to come to terms with loving a vampire, which goes against their training. This could lead to a lot of internal and external conflicts as they try to be together.
One plot idea could be that the Shadowhunters need to find a way to defeat a powerful demon that can only be weakened by a special type of music. So they seek out the Glee club. The Glee club members are hesitant at first but then realize the importance of their role. Another idea is that a spell gone wrong in the Shadowhunters' world sends some of their key characters to the Glee club's world. There, they have to adapt to high school life while also trying to find a way back. And the Glee club helps them blend in and in return, they learn about the Shadow World.
Well, perhaps it's a case of mistaken identity. A new character in Riverdale is kidnapped instead of the intended target, who was thought to be Archie because of his popularity. This could lead to a series of events where the other characters have to race against time to find the kidnapped person before it's too late. They might discover new secrets about the town and its inhabitants during the search.
One common theme is love. Magnus' relationships, especially with Alec, are often explored. Another is power. His magical powers and how they are perceived by the Shadowhunters are frequently a part of the stories. Also, acceptance. Magnus being a Downworlder, his fight for acceptance among the Shadowhunters and the mortal world is a common theme.
Maybe Bucky kidnaps Steve because he believes it's the only way to protect him. There could be a new and powerful threat that Bucky has discovered, and he thinks that by taking Steve away from the public eye and the Avengers, he can keep Steve safe. But Steve doesn't understand Bucky's motives at first and there's a lot of tension between them until Bucky can explain.
Another plot could be that Alexis kidnaps Castle as a prank that goes too far. She initially just wanted to teach him a lesson about being overprotective or something, but then things spiral out of control. Realizing her mistake, she has to find a way to fix the situation without getting in too much trouble.