It could be KAOS agents. They are always looking for ways to disrupt CONTROL, and kidnapping Max would be a major blow to them.
Another possibility is that it's a rogue element within CONTROL itself. Someone who has a grudge against Max or wants to take over his position might arrange for his kidnapping to further their own agenda.
It could be a jealous rival of the spirit animals' owners. This person might be envious of the special bond and powers that come with having a spirit animal and decides to kidnap them to spite the owners.
The Death Eaters are an obvious choice. They've always been after Harry, so they could easily be the ones to kidnap him. They'd want to take him to Voldemort to prove their loyalty and also to finally get rid of Harry for good.
The plot could involve Max being kidnapped by an old enemy from his past. This enemy might want revenge for something Max did before. His friends at CONTROL then have to race against time to find him. They follow a series of clues, like a mysterious note left at the scene of the kidnapping or a strange signal that Max manages to send out.
The Death Eaters are a likely choice. Since Snape was a double agent, some of them might have suspected his true loyalties all along. Once they got the chance, they would kidnap him to either punish him or to get information out of him about the Order of the Phoenix.
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.
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 Grimm could also be involved in an unusual way. Perhaps a new type of Grimm that has the intelligence to kidnap. They might be working with a human or Faunus villain who has some sort of control over them, and they take the character to an unknown location where the RWBY team has to face not only the Grimm but also the mastermind behind it.
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 kidnappers could be a group of hired mercenaries. Some powerful and wealthy person who has something to hide might have hired them. This person could be involved in illegal activities and Castle was on the verge of uncovering the truth, so they order the mercenaries to take Castle out of the picture.