It could be a rogue werewolf. Maybe this werewolf has a grudge against Stiles' pack and thinks that by kidnapping Stiles, he can get some sort of revenge or leverage.
There's also a possibility that it's a jealous rival. Someone who is envious of Stiles' relationship with his friends or his role in the group. This person might think that by kidnapping Stiles, they can take his place or cause chaos within the group.
It could be Zeref. Since Zeref has an interest in powerful magic users and Natsu is a strong dragon slayer, Zeref might kidnap Natsu to study his magic or use him in some dark plan related to his quest for immortality or power.
It could be an orc warband. Orcs have always been enemies of the elves, and they might see Legolas as a valuable captive either for ransom or to torture. Another possibility is a rogue wizard. Wizards who have turned to the dark side often seek powerful beings to experiment on, and Legolas, with his elven magic and skills, would be an interesting subject.
As mentioned before, Eggman is a likely candidate. He's always had his eyes on Tails' skills and would stop at nothing to use them for his evil plans. So he could be the one behind the kidnapping.
It could be a jealous rival. Maybe someone who has always been in competition with Shawn in some aspect of his life, like work or a hobby, and decides to take drastic measures by kidnapping him.
It could be a group of rogue Decepticons who are acting on their own. They might not follow Megatron's orders but still see value in kidnapping Arcee. Maybe they have a personal vendetta against her or think they can get rich by selling her to the highest bidder in the Cybertronian underworld.
It could be an envious rival. Maybe someone who's always been in the shadow of Osomatsu and his brothers and decides to take matters into their own hands by kidnapping Osomatsu. Another option is a deranged collector. This person might see Osomatsu as a rare item to add to their collection of oddities. Or it could be a vengeful spirit. In a more supernatural setting, a spirit with a grudge against the Matsuno family could kidnap Osomatsu as a form of revenge.
A group of outcasts from different islands might kidnap Moana. They feel that they have been wronged by the 'normal' society that Moana represents. They hope that by kidnapping her, they can get the attention they deserve and force the islands to change their ways. But Moana listens to their grievances and tries to find a way to help them while also finding a way home.
The kidnapper might be a jealous classmate who has been overshadowed by Boruto. This person could have snapped and decided to kidnap him to prove that they are better. It could also be a group of bandits who heard about Boruto's importance and thought they could get a huge ransom from Konoha for his return.
It could be Frieza. He might see Bulma as a valuable asset due to her intelligence and knowledge of Earth's technology. He could kidnap her to use her to build powerful weapons or devices to help him regain his power and dominance in the universe.
Perhaps a dark entity from another dimension. This entity might sense Yami's power and want to harness it for its own purposes, so it kidnaps him. There could be some sort of inter - dimensional struggle going on where Yami is a key piece.