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.
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.
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.
One possible villain could be Bizarro. Bizarro is always causing chaos and with Superboy and Superman together, it would be an interesting fight. Bizarro's reversed logic and powers would make it a tough battle for them.
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.
One plot idea could be that Lex Luthor's descendants kidnap Superman's son to use his Kryptonian powers for their evil experiments. They might hold him in a high - tech lair with various traps and defenses. Another could be that an alien race, jealous of Superman's influence on Earth, takes his son to force Superman to leave Earth forever. A third idea is that a powerful sorcerer from another dimension kidnaps the son to use as a bargaining chip to get Superman to retrieve a powerful magical artifact from a dangerous place.
Darkseid could be the main villain. Imagine Darkseid learning of Superman's ability to time - travel and using it to his advantage. He could try to invade different time periods to gain more power and resources. Superman would have to fight him across time and space to protect all of existence.
Lex Luthor would be a great choice. He's Superman's long - time nemesis. He could form an alliance with some of Batman's foes like the Joker. Luthor could use his intelligence and resources to create a plan that only Superman and Batman together could stop.