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.
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.
Well, if Misty joins Team Rocket in fanfiction, it would be a huge shock to the other characters. Her friends like Ash would be completely bewildered. Maybe she's been tricked into it somehow, like being deceived by Team Rocket's false promises. This could lead to some really interesting plot twists. For example, she might be used to set traps for Ash and the others, but deep down still have some good in her that causes internal conflict within Team Rocket.
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.
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, it could be that Team Rocket manages to brainwash the gym leaders into doing their bidding. Maybe they use some new, devious device or a powerful, mind - controlling Pokémon. The brainwashed gym leaders could then start causing chaos in the Pokémon world, like changing the rules of gym battles or stealing rare Pokémon for Team Rocket.
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.
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.
One potential consequence is that it would damage her relationships with her former friends. Ash and Brock would be very disappointed in her. Also, the Pokémon she had would be in a difficult situation. They might not be used to the unethical ways of Team Rocket. Another consequence could be that the balance of power in the Pokémon world would shift slightly. Team Rocket would gain a more competent member, which could make them more of a threat to other trainers and Pokémon centers.
Well, in such a fanfiction, the plot might involve Team Rocket devising a clever plan to capture Dawn. Maybe they use some new and devious Pokémon or traps. They could be after her Pokémon for some evil scheme, like using them to take over a Pokémon Contest Hall.
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.