A new villain could be a powerful and dark psychic - type Pokemon. This Pokemon could have the ability to turn Ash into a Pokemon as part of its grand plan to take over the Pokemon world. It sees Ash, who has always been a symbol of hope and a strong trainer, as a threat even in his human form. So, by turning him into a Pokemon, it hopes to disrupt the balance and order that Ash has been a part of maintaining.
Maybe a powerful and evil pokemon trainer who has a vendetta against Ash. Now that Ash is in a vulnerable pokemon form, this trainer could try to capture and control him. The trainer might have some dark motives related to using Ash's unique situation to gain power in the pokemon world.
Obviously, Ash would be one of the main characters since he's the one who turns into a Pokémon. His Pokémon partners like Pikachu would also be important. They might be confused at first about Ash's transformation but then help him adapt. And if we consider the 'lemon' as something non - adult related, there could be a new character, perhaps a wise old Pokémon that has some knowledge about Ash's transformation and guides him through this strange new phase.
It could be a jealous trainer. This trainer might see Ash in his shiny pokemon form and want that power for himself. So he tries to capture Ash by any means necessary, setting up all kinds of traps and challenges for Ash and his friends.
A jealous male trainer could be the main antagonist. He might see Ash's transformation as an unfair advantage given by some mysterious power. He constantly tries to undermine her in battles and challenges, believing that a female should not be as successful as a male in the Pokemon world.
A new evil organization could be created for the fanfiction. They could be a group of scientists who want to use Pokemon for their own cruel experiments. Angie and Ash find out about their plans and have to stop them before they harm too many Pokemon. They might be led by a mysterious figure who has a personal vendetta against Ash for some reason.
A powerful and greedy Pokémon collector could be the main villain. He wants to capture all the rarest Pokémon for his own collection, regardless of the harm it does to the Pokémon and their habitats. Ash and Caroline would have to stop him from achieving his evil goals.
In this fanfiction, if Ash turns into a pokemon, perhaps he becomes a Charmander. He could struggle with being in a different form. He might have to adapt to the life of a fire - type pokemon, facing challenges like being weak against water - type attacks and trying to find a way to change back while still having adventures with his friends, who now have to protect him in a different way.
Team Rocket could still be the main antagonists. They might see Ash as a Pikachu and try to capture him more than ever, thinking he's a special Pikachu. Maybe they believe he has some sort of new power because of his transformation.
It could be Team Rocket. They might have some sort of hold over Clemont, forcing him to betray Ash. Team Rocket has always been after Ash's Pikachu, and using Clemont to get to Ash would be a devious plan for them.
Team Rocket would be a likely main villain. They are a big part of the Pokemon Red and Blue story, and when Ash enters this world, they would surely cause trouble for him. Their schemes to steal Pokemon and take over the world would be a direct threat to Ash and his new friends.