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.
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.
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.
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.
One common theme is redemption. Many fanfics explore the idea of Team Rocket members turning over a new leaf. Another theme is power - seeking. Since Team Rocket is always after powerful Pokémon, this often features in fanfics.
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.
Sure. 'The Rocket Resurgence' is a great one. It focuses on Team Rocket's attempts to regain their former glory in a new region. Another interesting fanfic is 'Team Rocket's Redemption Arc' which shows a different side of the usually villainous team, exploring their possible paths to redemption.
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.
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.