There could be a new, unknown dark wizard who has infiltrated the Order. This wizard could be the main villain. They use the Order's resources and good intentions to get Harry kidnapped. Once they have Harry, they plan to use his power for their own dark purposes. The Order is oblivious to this new threat within their ranks, and Harry has to figure out who this villain is and stop them while also dealing with being kidnapped by the people who were supposed to protect him.
It could be a rogue member of the Order. Maybe someone who has their own agenda and decides that Harry is a threat to their plans. So they manipulate the Order into kidnapping Harry, but then they have their own evil intentions for him.
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.
It could be a rogue Death Eater who escaped punishment and has been biding his time. He might have a new, more insidious plan to bring back the dark ways of Voldemort.
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.
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.
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.
It could be a new dark wizard who has been secretly plotting in the shadows. This wizard might be jealous of Harry's fame and power, and decides to make him disappear so that he can rise to power unopposed. He could have a group of followers who are experts in dark magic and are able to carry out his plan to make Harry vanish.
The Queen of Hearts would make a great main villain. Her tyrannical rule and quick temper in the original Wonderland story could be amplified in a fanfiction. She could be a powerful dark magic user who sees Harry as a threat to her rule and tries to stop him from achieving his goals in Wonderland.
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.