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.
Giovanni is usually a main character. He's the leader of Team Rocket and in the Rainbow Rocket scenario, he's a central figure. Lysandre from Team Flare could also be a main character. His extreme views and his connection to the Rainbow Rocket's overall plan make him important. And of course, the protagonist of the fanfic, who could be a young trainer trying to stop their evil plans.
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.
In a Pokemon Red join Team Rocket fanfic, the main character could be a disillusioned trainer. Maybe they've lost a few too many battles and are looking for a new way to gain an edge. Team Rocket seems like an alluring option. They join up and are immediately thrust into the world of illegal Pokemon trading. However, they soon meet a friendly Pokemon that shows them kindness despite their new allegiance. This makes them question their decision to join Team Rocket and they start to think about how they can use their new position to actually help the Pokemon instead of harming them.
Maybe there's a rogue Pokemon trainer. This trainer is jealous of Dawn's skills and the attention she gets. When Dawn joins Team Rocket, this trainer sees it as a chance to expose her as a fraud. He or she then tries to stop Dawn and Team Rocket's activities, thinking that they are up to no good, which they are, but the trainer has his own self - centered motives.
Misty's Pokemon could be involved in a way where they are all captured by Team Rocket. Then Misty has to rely on her wits and some basic Pokemon - handling skills without her actual Pokemon. She has to find a way to free them. Meanwhile, her Pokemon are trying to communicate with other wild Pokemon in Team Rocket's base to create a sort of uprising. This would lead to a big showdown where Misty and her freed Pokemon take on Team Rocket and their own captured Pokemon.
One possible plot could be that Misty gets captured by Team Rocket. They plan to use her as a bargaining chip against Ash. But during her captivity, she manages to befriend some of the lower - level Team Rocket grunts. These grunts start to have second thoughts about their evil deeds because of Misty's influence. Eventually, Misty uses this new - found friendship to escape and also cause some internal chaos within Team Rocket.
One idea could be exploring the backstories of the Rainbow Rocket members in more detail. For example, Giovanni's motives and how he assembled the team. Another could be a scenario where the protagonist has to infiltrate the Rainbow Rocket base. Maybe they have to find a way to stop a new, more powerful weapon the team is developing.
One interesting Pokemon Team Rocket fanfiction could be about a Team Rocket member who has a change of heart. For example, they might start to see the beauty in the relationship between trainers and their Pokemon and decide to secretly help the heroes instead of causing trouble.
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.