As mentioned before, it could be rogue skitters. They are often portrayed as a threat in the show, and kidnapping Matt would be a strategic move for them.
It could be Hacker. He's always causing trouble in Cyberchase and might see Matt as a threat or someone he can use for his evil plans. Maybe he wants to force Matt to help him take over more digital territories.
Maybe in the fanfiction, Matt is kidnapped by an unknown alien faction that has just arrived on Earth. This new group might not be aware of the complex relationships on Earth and simply take Matt because he was in the wrong place at the wrong time. They could be studying humans and think Matt is a good specimen to start with. Also, it could be that a group of desperate survivors, in need of supplies, kidnap Matt thinking they can trade him for what they need from the main group in 'Falling Skies'.
It could be a rival spy agency. They might see Moneypenny as a valuable target to get information about MI6's operations. They would likely be highly trained and well - equipped.
Maybe it's a character from one of the games Matpat has theorized about. For example, if he made a theory about a game villain being more complex than thought, that villain could come to life in the fanfiction and kidnap him to prove his own power and intelligence.
The kidnapper might be a deranged Toad. Maybe this Toad has been corrupted by some evil force and decides to kidnap Luigi for reasons only known to the twisted mind of this new 'evil Toad'.
It could be Dr. Eggman. He's always after Sonic and would love to get his hands on him to stop Sonic from foiling his evil plans. He might want to study Sonic's speed and use it for his own machines.
The kidnapper could be a former ally who has turned against Luffy. Maybe they've been corrupted by power or some other force. They believe that by kidnapping Luffy, they can take over the Straw Hat Pirates or get their hands on valuable resources that Luffy has access to.
It could be Frieza. Frieza has a long - standing grudge against the Saiyans, especially Vegeta. He might kidnap Vegeta to torture him or to use him as a bargaining chip against the other Saiyans. Another possibility is Cell. Cell might see value in Vegeta's genetic material and kidnap him to extract it for his own evolution.
It could be an enemy from one of his past cases. Someone who holds a grudge against L for getting them caught or ruining their plans before.
There's a chance it could be a character with a hidden agenda within her own circle. Maybe someone who seems friendly on the surface but has ulterior motives. They kidnap her to further their own goals, which could be related to power or money within their community.