It could be a rival group. Maybe a group of villains who are jealous of Morgan and Peter's abilities or something they have. For example, if they are super - powered in the fanfiction, the villains might want to study them or steal their powers.
A new, mysterious group of poachers could be the villains. They might be after rare and powerful Pokemon to sell them on the black market. These poachers could be highly organized and have advanced technology to capture and keep the Pokemon hidden. Another option could be a lone, power - hungry trainer who believes that by kidnapping the strongest Pokemon, they can become the ultimate Pokemon master. They might not care about the well - being of the Pokemon, only seeing them as tools to achieve their own goals.
One possible plot could be that their friends have to embark on a dangerous rescue mission. They might have to solve a series of puzzles or clues left by the kidnappers to find where Morgan and Peter are being held.
An evil scientist could be a possible villain. The scientist might believe that Jellybean has some unique genetic trait that they want to study. So they kidnap her to perform experiments on her. This would lead to a story where her friends have to break into the scientist's secret lair to rescue her.
Peter could be a character with some heroic or special qualities. He might be a young man with a big heart. Morgan could be a young girl, perhaps a student at the school. They could have a special bond, like an older brother - like figure (Peter) and a younger sister - like figure (Morgan).
In a more fantastical setting, it could be a magical being who has some sort of vendetta against Peter or Michelle. Maybe they accidentally disrupted some magical ritual or offended the being in some way, and now the being wants to use their kidnapping as a form of punishment or to get something from them.
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.
It could be a rival family. They might be jealous of the Castle family's status or wealth and decide to kidnap them to gain an upper hand. For example, if the Castle family owns a large business empire, the rival family could kidnap them to take over the business.
It could be a group of outcast Lost Boys who have turned bad. They might be jealous of Wendy's special place in Peter's heart and in the group. So they kidnap her in an attempt to show Peter that they are in control now and can disrupt the harmony of the group.
Maybe Pepper Potts could find out what Tony has done and rescue Peter. She might be able to talk some sense into Tony and make him release Peter.
Hans could be a likely villain in these fanfictions. Since he already had evil intentions in the movie, it's easy to imagine him coming back to kidnap Anna for revenge or to try and take over Arendelle again. Another one could be a power - hungry sorcerer from a far - off land who wants to use Anna as a bargaining chip against Elsa.