In a more fantastical setting, it could be a magical being who has some sort of vendetta against Peter or Michelle. Maybe they accidentally disrupted some magical ritual or offended the being in some way, and now the being wants to use their kidnapping as a form of punishment or to get something from them.
It could be a group of outcast Lost Boys who have turned bad. They might be jealous of Wendy's special place in Peter's heart and in the group. So they kidnap her in an attempt to show Peter that they are in control now and can disrupt the harmony of the group.
The villain could be a jealous ice - mage who wants Elsa's powers all to himself. He sees Elsa as a threat to his own dominance in the world of ice magic.
One plot idea could be that Peter is kidnapped by an unknown group and Michelle sets out to rescue him. She could use her wits and some detective skills she has learned over time. Maybe she teams up with some of Peter's friends from school or work.
A rogue ninja from another village who is jealous of Ino's talents and the reputation of her village could be the villain. This ninja might think that by kidnapping Ino, they can bring down the morale of her village and prove their own superiority.
A mad scientist - type character could be the villain. He might be obsessed with creating the perfect virtual being and sees Hatsune Miku as the key. So, he kidnaps her to run all kinds of experiments on her code. He wants to extract her unique singing ability and transfer it to his own creations.
It could be a new villain who is trying to make a name for themselves by targeting a popular hero like Present Mic. They might see him as an easy target to get attention.
Maybe Doctor Octopus. He has always been obsessed with power and knowledge. He might kidnap Peter to figure out the secret behind his spider - powers. He could think that by studying Peter, he can enhance his own mechanical arms or gain some new form of power that would make him the most feared villain in the city.
It could be a rival group. Maybe a group of villains who are jealous of Morgan and Peter's abilities or something they have. For example, if they are super - powered in the fanfiction, the villains might want to study them or steal their powers.
The Joker is a likely suspect. He loves to target Batman's loved ones to mess with him. He might use the kidnapping as a way to draw Batman into a twisted game, setting up elaborate traps along the way.
Brainiac could be the villain in a Superman's son kidnapped fanfiction. Brainiac is known for his thirst for knowledge and power. He might kidnap the son to study his Kryptonian physiology and powers. Zod, another Kryptonian, could also be a culprit. He may have different ideas about how to raise a Kryptonian on Earth and decides to take Superman's son to implement his own vision. Additionally, a new, original villain created specifically for the fanfiction could be the kidnapper, perhaps a mad scientist who wants to create a hybrid using Superman's son's DNA.