Definitely Ash. His journey and how it's affected by the transformation can be the heart of the story. Team Rocket has so much potential. They could be the cause of the transformation, or they could be accidental victims too. Another character worth focusing on is Tracey. He's not as well - known as some of the others, but that could be used to an advantage. He could be the one who discovers a hidden aspect of the transformation. And don't forget about the Pokémon in the Pokémon Center. They could be witnesses to strange happenings related to Ash's transformation and could play a small but important role in the overall fanfiction.
One idea could be that Ash gets transformed into a Pokémon and has to figure out how to communicate with his friends. Another could be that Team Rocket manages to use a new device to transform Pikachu into a different type of Pokémon. Maybe Ash and Team Rocket end up having to team up when a new, more powerful villain emerges who wants to transform all Pokémon into mindless servants.
Ash is obviously one of the most popular characters. He's the main character of the Pokemon anime, and in fanfictions, his adventures with or against Team Rocket are always interesting. People like to see how he reacts to different situations that Team Rocket creates or how he manages to outwit them.
If Team Rocket turns Ash into a Pokemon, it could lead to a really interesting story. Ash would have to experience the world from a Pokemon's perspective. He'd understand their struggles, like being caught and trained. This could also be a way for him to better understand his own Pokemon and their bond with him. And it would be a wild adventure as he tries to find a way to turn back to his human form.
In a fanfiction where Ash joins Team Rocket, it could lead to some really interesting storylines. Ash has a lot of knowledge about Pokémon training that Team Rocket lacks. He could potentially teach them new techniques, but at the same time, his moral compass would be constantly at odds with their devious ways. Maybe he joins them because he's somehow tricked or he has his own secret plan to take them down from the inside. It would be a great opportunity to explore different aspects of his character and how he adapts to this new situation.
Obviously, Ash and Jessie, James, and Meowth from Team Rocket are the most popular. Ash is the main hero, and the Team Rocket trio is always causing trouble for him, so they are central to most fanfictions in this theme.
Jessie and James are the obvious ones. They are the main members of Team Rocket. Jessie could be constantly trying to outdo Ash in Pokémon battles or contests of skill. James, on the other hand, might be more conflicted about having Ash around. He could secretly admire Ash's kindness towards Pokémon and start to have second thoughts about their Team Rocket activities.
Jesse and James from Team Rocket are always interesting. Their use of hypnosis adds a new layer to their already complex characters. They become more menacing when they can hypnotize their opponents. Also, Ash can be an interesting character in this context. His determination to break free from hypnosis or protect his Pokemon from it shows his strong will. And Pikachu too. Imagine Pikachu trying to fight off the effects of hypnosis while still being its cute and powerful self.
If Team Rocket turns Ash into a Pokemon, his relationship with his old Pokemon would change. His Pokemon might not recognize him at first. But as they sense his familiar spirit, they could try to protect him. And Ash, in his new form, could learn a lot about the true nature of Pokemon. He could discover secrets about their evolution, abilities, and the hidden powers within them that he never knew as a human trainer.
One thing that would happen is that his Pokémon battles would take on a whole new meaning. Instead of battling for the sake of becoming a Pokémon master, he might be battling to further Team Rocket's goals. His Pokémon would have to adjust to this new purpose. Also, Ash would probably have to wear Team Rocket's uniform, which would be a really strange sight for fans who are used to seeing him in his normal get - up.
One interesting storyline could be Team Rocket actually helping Ash in a dire situation. Maybe they realize that a greater evil is about to destroy the Pokemon world and they decide to team up with Ash for once. Their skills in stealing and sneaking around could be useful in gathering information about this new threat.