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.
There could be a mad scientist - type villain. This person could be kidnapping Pokemon to conduct cruel and unethical experiments on them, hoping to unlock some sort of ultimate power or knowledge. They might be operating from a hidden lair, surrounded by all sorts of strange machinery and captured Pokemon. Or it could be a vengeful spirit or entity that has some sort of grudge against Pokemon or their trainers and starts kidnapping them as a form of revenge.
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.
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.
Perhaps a powerful and corrupted Pokemon could be behind the kidnapping. This Pokemon might be under the control of an evil force or it could have its own motives. It could sense Lillie's special connection to Pokemon and want to use her for its own gain, like increasing its power or finding a way to rule over other Pokemon.
A group of poachers could be the kidnappers. They might think that Serena has information about the location of rare Pokemon in the areas she has traveled. They want to use her to find these Pokemon so they can capture and sell them on the black market.
The obvious villains could be the malfunctioning animatronics from FNAF. They could be acting under some sort of dark influence and see Ash and his Pokemon as intruders to be eliminated.
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.
Another option is a random criminal who just sees May as an easy target. He might not even be related to the Pokemon world initially but realizes that he can ransom her to her wealthy Pokemon - loving family or friends. However, he soon finds out that dealing with a Pokemon trainer's friends is not as easy as he thought.
A young and determined trainer could be the hero. They have a strong bond with their Pokemon and when their Pokemon are kidnapped, they are furious and won't stop until they get them back.
There could be a secret organization that believes the chosen one's power will disrupt the balance they have carefully maintained in the Pokemon world. They would be villains as they try to eliminate the chosen one and the Pokemon helping them, thinking they are doing what's best for the world but in a very wrong way.
It could be the well - known Team Rocket. They are always up to no good and kidnapping Pokemon for their own gain is right up their alley.