There's also a possibility that it's a group of thieves. They might think that Peter, being a smart student, has access to valuable technology or information. Flash just happens to be with Peter at the wrong time and they both get kidnapped.
Maybe it's an old enemy of Peter's who has found out about his friendship with Flash. For example, someone from Oscorp who wants to take revenge on Peter for foiling their evil plans in the past and figures kidnapping Flash will draw Peter out.
Maybe Doctor Octopus. He has always been obsessed with power and knowledge. He might kidnap Peter to figure out the secret behind his spider - powers. He could think that by studying Peter, he can enhance his own mechanical arms or gain some new form of power that would make him the most feared villain in the city.
In the fanfiction, they might be kidnapped by a supervillain who wants to use them as bait to lure Spider - Man. Maybe the kidnapper thinks Flash has some connection to Peter Parker (aka Spider - Man) and plans to expose his identity through Flash.
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.