In a 'Bonnie joins Team Rocket' fanfic, the plot might start with Bonnie feeling left out or misunderstood in her normal group. Team Rocket takes advantage of this. As she joins them, she starts to learn their secrets. But then she has to decide if she wants to stay with them or go back to her old friends, and this decision could be the main conflict throughout the story.
One popular 'Bonnie joins Team Rocket' fanfic might be on FanFiction.net. You can search there using those keywords. Usually, fanfics with this concept explore how Bonnie's character changes when she aligns with the villains. It could be really interesting to see her interactions with Jessie and James.
Another theme is the clash of good and evil. Bonnie represents the good side with her pure heart, while Team Rocket is the bad guys. Their interactions often play on this dynamic, with Bonnie sometimes trying to reform them or at least understand why they do bad things.
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.
There's a fanfic titled 'Bonnie and Team Rocket: Unlikely Allies'. In this one, Bonnie somehow ends up working with Team Rocket for a short while, leading to some really interesting character interactions. It shows how Bonnie's naivete and Team Rocket's deviousness can create both humorous and tense situations.
Ash joining Team Rocket could lead to some interesting character dynamics. He might start to question his own values. For instance, he's always been about friendship with Pokemon, but Team Rocket is more about using them for gain. This internal conflict could be a major part of the fanfic. Also, his relationship with Jessie, James, and Meowth would change drastically.
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.
Ash might start to become more devious. He could learn some of Team Rocket's underhanded tactics, which would be a big change from his usually straightforward and honest self. But at the same time, he could also be a force for change within Team Rocket, slowly making them less evil.
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.