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.
A plot twist could be that there's a secret organization within Team Rocket that Ash and Misty discover. This organization has different motives than the regular Team Rocket members. They might end up having to choose between the original Team Rocket's goals and this new secret group's goals. Also, it could be that Ash and Misty's joining was all part of a prophecy in the Pokémon world, which no one knew about until they actually joined Team Rocket.
The plot might involve a power struggle within Team Rocket. Ash and Misty could be brought in because they possess certain skills or knowledge. For example, Ash's bond with his Pokémon could be seen as a valuable asset. Misty's understanding of water - type Pokémon might also be desired. However, they soon realize that they are being used in a power play between different factions of Team Rocket, and they must decide which side to take or find a way to break free from the whole mess.
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.
Well, one plot twist could be that Ash is actually a double agent. He pretends to join Team Rocket to gather information for the good guys. Maybe he discovers a big secret plan of Team Rocket, like they're planning to steal all the Pokeballs in a certain region. This would completely change the power dynamic and put Team Rocket on high alert.
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.
Ash's character might become more conflicted. He has always been the hero, fighting against Team Rocket. But now, being part of them, he would question his own values. He might initially try to change Team Rocket from the inside, but as he faces more and more of their evil deeds, he would struggle between his loyalty to his new 'team' (out of a sense of obligation since he joined) and his true nature of being a Pokémon protector. Misty, on the other hand, would probably be more outspoken about her dislike for Team Rocket's actions and try to convince Ash to leave sooner.
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.
It could lead to some really unexpected and exciting plot twists. Ash's alignment with Team Rocket would completely change the dynamics of the story.
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.
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 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.