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.
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.
The plot might involve Ben being captured by a new and powerful alien race. They could be interested in the Omnitrix technology. Ben would have to figure out their weaknesses while being held captive, and perhaps make some unexpected allies among the other captives. He'd then use his wits and the powers of the Omnitrix to break free and save the day.
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.
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.
Well, if the captor is a child, the fairy might try to trick the child into letting it go. It could tell tall tales about having great treasures hidden in the forest. If the captor is an adult with malicious intent, the fairy would be very defensive and try to hide its magic from being exploited, while constantly looking for a chance to break free.
It might be a powerful magical being. This being could be on a mission to study the Powerpuff Girls' powers and in the process of capturing Bubbles, realizes she has a very special personality. He is intrigued by her and as they interact more, love blossoms between them.
The Sultan himself could capture Aladdin if he were misled into believing that Aladdin was a threat to Agrabah. Maybe some false rumors were spread about Aladdin planning to overthrow the Sultan. So, the Sultan, out of fear for his kingdom and his daughter, orders Aladdin's capture.