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.
Another possibility is that it could be an older, forgotten character from the Naruto universe. Someone who was once on the sidelines but now has a new role as the chosen vessel. It could be a character from a minor clan that has some long - lost power that makes them suitable for this important position.
Maybe the chosen one has to solve a mystery that threatens the Pokemon world. The Pokemon use their different types of skills like water - type Pokemon using their ability to explore underwater areas to find clues. Fire - type Pokemon can keep the chosen one warm in cold and dangerous places while they search for answers.
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.
The Chosen One is, of course, the main character. They are usually a young trainer with a big heart and a strong sense of justice. There are also often wise mentors, like an old Pokemon Professor or a retired champion who guide the Chosen One.
The Chosen One is obviously a main character. They are the central figure around which the story revolves. Their personality could be that of a brave and determined trainer, always ready to face challenges.
Team Rocket could still be the main antagonists. Even though they usually have comical failures, in this fanfiction, they could discover Ash's connection to the legendary Pokemon and try to use it for their own evil plans. Maybe they want to capture the legendary Pokemon through Ash or steal the power that Ash has because of his chosen - one status.
Ash as the Chosen One in Pokemon fanfiction is a really interesting concept. It gives a whole new layer to his character. He could be given a special Pokemon by some mysterious force that is crucial for his destiny. This Pokemon might be one that no one has ever seen before. His friends would also play different roles, perhaps as protectors or guides to help him fulfill his chosen - one duties. And his battles would become even more epic as he has this greater responsibility on his shoulders.
There could be a new, unknown group of villains in the fanfiction. They might be after a special type of Pokemon that is native to Unova. These villains could be using underhanded tactics to catch these Pokemon, and Ash and May would have to uncover their motives and stop them. For instance, they could be trying to use the power of these Pokemon for their own selfish gains, like taking over Unova's Pokemon centers or disrupting the Pokemon league.
Maleficent could be a great villain in this fanfiction. Her connection to dark magic makes her a natural fit for the setting of the prison of darkness. She could be the one who put Kairi there or be trying to manipulate her for her own evil plans.
Ash is definitely one of the main characters since it's about him being the chosen one. His Pokémon partners like Pikachu are also likely to be main characters as they would be involved in his journey as the chosen one.