There's also a possibility that it's a group of antagonists working together. They could be from different factions but united by their hatred for Sora. They might have different motives for the capture, like one wants Sora's power, another wants to use him to control his friends, etc.
Maybe it's an old foe who has managed to regain power and wants to make Sora pay for past defeats. For example, a powerful dark sorcerer who was once defeated by Sora but has now found a way to capture him through some devious plot.
There's a possibility that it's a villainous trainer. This trainer might capture Gengar with the intention of using it for evil purposes, like using Gengar's powers to steal other Pokémon or cause chaos in Pokémon battles.
It could be the Blackbeard Pirates. Since they have a history with the Whitebeard Pirates, they might capture Marco to get information or as a form of revenge.
Well, in such a fanfiction, Sora might be held in a dark and gloomy dungeon. Maybe some old enemies from the original story could be behind the capture, seeking revenge.
It could be the Marines. They've been after Luffy for a long time, so it's possible they finally manage to capture him in this fanfiction.
It could be the League of Villains. They've always been interested in taking down heroes and Deku, as a rising hero, would be a prime target for them.
It could be Captain Hook. He has always been Peter Pan's nemesis and has a strong motive to capture him. Maybe he wants to finally get revenge for all the times Peter has outsmarted him.
It could be Discord. He loves causing chaos and might capture Twilight Sparkle just for the fun of it or to disrupt the harmony in Equestria.
Maybe a rogue ninja group that wants to sell Naruto to the highest bidder. They see him as a valuable asset due to his strength and status in Konoha.
Maybe it's an old foe who has come back with a vengeance. For example, a gem that Steven thought he had defeated before might return and capture him in order to get revenge. This foe could have some new abilities or powers that make it difficult for Steven to escape.
It could be a rival group. They might be jealous of Serena's abilities or resources and capture her to gain an advantage.