A group of smugglers could be the kidnappers. They accidentally stumble upon a Sith in hiding and decide to take the Sith hostage. They think they can sell the Sith to the highest bidder, not realizing the danger they've put themselves in until it's too late.
Bounty hunters could be the kidnappers. They might be hired by a powerful political figure who wants to use the Sith's knowledge or power for their own gain. The bounty hunters would have to deal with the Sith's attempts to escape and the possible pursuit by other Sith.
It could be the Jedi. They might kidnap a Sith in order to prevent a major dark side plot. They would try to rehabilitate the Sith or at least keep them out of harm's way until they figure out how to deal with the situation.
The First Order is a common kidnapper in such fanfictions. Since Rey is a powerful Force - user and a threat to their regime, they might try to kidnap her to either turn her to their side or simply eliminate her. They have the resources and the motivation to carry out such an act.
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.
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 the Separatists. They might see Anakin as a valuable hostage to use against the Jedi and the Republic. His skills as a Jedi Knight make him a prime target for them to gain some sort of leverage in the war.
Perhaps a rival community. They might feel threatened by Carl's group and think that by kidnapping Carl, they can gain an advantage. They could be more organized and have a specific plan in mind, like using Carl to get access to their resources. It could also be a group of escaped prisoners. They have no moral compass and figure that kidnapping Carl can help them get whatever they want in this lawless world.
It could be a rival family who wants to use Tsuna as a bargaining chip against his own family.
It could be some rogue Hollows who see Ichigo as a big threat and think that by kidnapping him, they can eliminate that threat.
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.
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 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.