Well, in the 'Ash and Misty joins Team Rocket fanfic', they could be brainwashed by Team Rocket's technology or some devious plan. Once they join, they might be given new uniforms and tasks. They could be involved in stealing Pikachu again, but this time from the other side. It would create a whole new dynamic in the Pokémon world, with their old allies now becoming their enemies.
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.
One possible plot twist could be that Ash and Misty are actually undercover for a greater good. They pretend to join Team Rocket to expose their big plans from the inside. Another twist might be that they are forced to join because Team Rocket has kidnapped their Pokémon friends. So, they have to play along to save them.
The main characters might not only be human trainers. Some Pokemon could take on leading roles. For example, a powerful and wise Charizard could be a main character. It might have been trained by a famous trainer in the past but now fights independently against Team Rocket. There could also be a group of Eeveelutions that are the main focus. They have different abilities and personalities, and together they form a force to be reckoned with against Team Rocket. Alongside them, there could be a trainer who acts as a guide or coordinator for their efforts.
Well, the plot might start with a trainer who is a bit of a rebel. They don't like following the normal rules of the Pokemon world. Team Rocket notices this and recruits them. As part of Team Rocket, they participate in raids on Pokemon Centers to steal medicine for their own Pokemon. However, during one of these raids, they encounter a very sick Pokemon that needs that medicine desperately. This makes them question Team Rocket's motives. They then start to secretly work against Team Rocket from within, trying to protect the Pokemon and the integrity of the Pokemon world.
They could also change Team Rocket for the better. Maybe they would introduce a new sense of honor or fairness. Ash's determination and Misty's feistiness could influence the other members to be less about pure evil and more about having fun in their villainous deeds. In a fanfiction, this could lead to some really interesting character development for both Ash, Misty and the Team Rocket crew.
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.
A possible plotline is that some Pokemon start to develop new strategies against Team Rocket. They might learn to communicate better with humans to coordinate attacks. For instance, the Psychic - type Pokemon could use their powers to read the Rockets' minds and share the information with the other Pokemon and trainers. Also, there could be a story where a group of orphaned Pokemon form a resistance against Team Rocket. They have to rely on their wits and natural abilities as they don't have trainers to guide them, making their fight even more heroic.
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.
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.