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.
It could be Team Rocket. They've always been after Ash and his Pikachu. They might finally succeed in capturing him and then Pikachu has to come up with a plan to rescue Ash.
Another possibility is a group of corrupted Plumbers. They turn against Ben and capture him, perhaps because they want to use the Omnitrix for their own evil purposes. They would have knowledge of Ben's abilities and how to contain him, which would make for an interesting conflict.
Maybe some mad scientist who wants to experiment on Beast Boy's shape - shifting DNA. He could be looking for a way to transfer the ability to himself or create some sort of mutant army. Another option is that it's a group of aliens who mistake Beast Boy for a dangerous creature and capture him to study. They might not understand that he's a sentient being with friends who will come looking for him.
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.
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.
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, Peter Pan might be in a really tough situation. He could be locked up in Captain Hook's lair on the pirate ship. Maybe Hook would try to break Peter's spirit, but Peter being Peter, he'd surely find a way to outwit Hook eventually.
A different 'Peter Pan Captured' fanfiction might involve Peter being captured by pirates. Hook could have a new elaborate plan this time. But Peter, even in captivity, might find a way to communicate with the magical elements of Neverland like the mermaids, who then help him escape.
It could also be a new character, perhaps a dark sorcerer who is jealous of the magic in Neverland. This sorcerer might target Emma because she has an unknown power within her that could disrupt his own plans for the magical world. He would try to separate her from Peter Pan and use her power for his own evil deeds.