It could be a criminal mastermind who sees Shinichi as a threat to his illegal activities and Kaito as someone who can be used as leverage. Maybe a powerful underworld figure who has been on Shinichi's radar for a long time and decides to take action by kidnapping them both.
There could also be a group of villains working together to kidnap Sonic. For instance, a combination of Eggman and some of his more powerful robot creations along with a couple of other villains from Sonic's rogues gallery. They might have a grand plan that requires Sonic's capture, like using his power to open a portal to a world full of chaos energy that they can then control.
A jealous rival of Inuyasha might kidnap Kagome. For example, another demon who wants Inuyasha for himself might think that by taking Kagome, he can get Inuyasha to do his bidding. This would create a lot of drama and conflict between Inuyasha and the kidnapper.
The Naraku would be a likely kidnapper. He is always plotting against Inuyasha and trying to get his hands on the Tessaiga. Kidnapping Inuyasha would be a way for him to either steal the sword or find a way to break Inuyasha's spirit so that he can no longer oppose him.
It could be a secret society that has been observing their actions and sees them as a threat to their hidden agendas. This society might have members with special skills and resources to carry out the kidnapping.
A secret society that believes Mycroft is a threat to their hidden agendas. They may think that by kidnapping him, they can stop him from interfering with their plans. They would likely be very well - organized and have resources to keep him hidden.
The Joker is a likely kidnapper. He has a history of causing chaos and targeting the Bat - family. He might see kidnapping Batgirl as a way to get back at Batman or just for his own twisted amusement.
It could be a rival athlete who is jealous of Serena's success. They might think that by kidnapping her, they can eliminate the competition. Another possibility is a deranged fan who has an unhealthy obsession with Serena and wants to keep her all to themselves.
The Yiga Clan could be likely kidnappers. They've always been enemies of Link and would love to get their hands on him. They might see kidnapping him as a way to stop him from interfering in their plans. Another possibility is the Gerudo thieves. Although not all Gerudo are bad, there could be a group of them who think Link has something valuable and decide to take him hostage.
The Death Eaters are very likely kidnappers. Since they are Voldemort's followers, they might try to kidnap Harry to please their master or gain some advantage in the wizarding war. Another possibility is some power - hungry pure - blood wizards who see Harry as a threat to their status quo. They could kidnap him to keep him out of the way.
It could be a group of rogue ninjas. They might see Shikamaru as a valuable asset due to his intelligence and strategic skills. They could plan to sell him to the highest bidder or use him to carry out their own devious schemes.