A great plot idea could be that there's a strange energy wave that causes Ash and Team Rocket to swap abilities. Ash now has Team Rocket's knack for creating contraptions and Team Rocket has Ash's Pokémon training skills. This would lead to a lot of comical and also intense situations. Ash might use his newfound skills to create a device to reverse the transformation. Meanwhile, Team Rocket could be using their Pokémon training skills to try and catch Pikachu in a more strategic way than just using their usual traps. There could also be a sub - plot where the Pokémon themselves are confused by the changes in their trainers.
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.
There could be a fanfiction where Team Rocket finally manages to steal all of Ash's Pokémon. But instead of using them for evil, they realize the strong bond between Ash and his Pokémon and start to have a change of heart. This would be a great exploration of the themes of redemption and the power of friendship in the context of the Ash vs Team Rocket dynamic.
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.
One idea could be that Ash feels betrayed by his friends because they always overshadow his achievements. So, in a fit of anger and disappointment, he decides to join Team Rocket. He might think that with their resources, he can finally become a more powerful trainer on his own terms.
One idea could be creating an OC who was originally a regular Trainer but got corrupted by Team Rocket's ideals. For example, they might have lost a big Pokemon battle and felt so defeated that they were easily swayed by Team Rocket's promises of power. Another idea is an OC who is a double agent within Team Rocket, secretly working for the good guys to bring down the organization from the inside. They could have a unique Pokemon partner that helps them in their undercover work.
One idea could be that Ash, as the leader of Team Rocket, uses his knowledge of Pokémon in a new way. He might focus on stealing rare Pokémon not just for evil purposes but to prove a point about Pokémon training ethics. For example, he could target trainers who mistreat their Pokémon and then 'liberate' the Pokémon into a better environment he creates. Another plot could involve Ash leading Team Rocket in a new direction of cooperation with other Pokémon organizations. Instead of always being the bad guys, they could form alliances to solve some of the more complex problems in the Pokémon world, like dealing with a new, powerful and dangerous Pokémon species that threatens the balance of nature.
Well, if Ash joins Team Rocket in a fanfic, it would be a huge shift in the Pokemon world. His friends, like Misty and Brock, would be shocked. They might try to rescue him. Ash, on the other hand, could initially be attracted to the idea of a new adventure with Team Rocket. He could see them as underdogs in a way, always failing but still trying. But as time goes on, he'd start to see the problems with their way of doing things.
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.
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.
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.
One possible plot could be Ash getting brainwashed by Team Rocket into thinking his Pokémon friends are his enemies. Then he starts to help Team Rocket in their schemes against other trainers. This would create a lot of conflict as his real friends try to snap him out of it.