Well, there are several consequences. Firstly, Misty's reputation as a good - natured trainer would be ruined. People in the Pokémon world who knew her would be shocked and lose trust in her. Secondly, from a story - telling perspective, it would create a lot of drama. Ash would probably try to rescue her or convince her to come back. And Team Rocket might use her knowledge of Ash's strategies against him. Lastly, Misty herself might start to change her personality. The influence of Team Rocket could make her more cynical and less empathetic, which is a big change from her original character.
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.
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.
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.
The Pokémon League would be in shock. They would see Ash and Misty as traitors and would probably send out teams to capture them. Pokémon trainers who looked up to Ash would be very disappointed. They might start to question their own values and the values of the Pokémon training 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.
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.
Obviously, Dawn and the members of Team Rocket like Jessie, James, and Meowth are the main ones. But there could also be Dawn's Pokémon, like Piplup, which might try to rescue her. And there could be other Pokémon trainers or characters from the Pokémon world who might get involved in the rescue mission.
One possible plot for a fanfic where Ash joins Team Rocket could be that there's a powerful and mysterious Pokémon that only Team Rocket knows how to find. Ash, desperate to catch this Pokémon, makes a deal with them to join. However, once he's part of the team, he discovers that their methods are far more cruel than he expected. He then has to battle his own conscience as well as the other members of Team Rocket to either stop their plan or find a more ethical way to catch the Pokémon.
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 common theme is the power struggle. Team Rocket uses hypnosis as a tool to gain an upper hand in their devious plans against Ash and his friends. For example, they might try to hypnotize Pikachu to steal it. Another theme could be the moral dilemma. The characters who are hypnotized often face a battle between their true selves and the commands implanted by the hypnosis. It also often features the idea of breaking free from the hypnosis, showing the strength of the bond between Pokemon and their trainers.