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.
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.
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, 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.
Yes, in some Team Rocket fanfictions, Ash can be depicted in various ways that might involve him having some sort of connection to Pokémon in a different light. Maybe he could be experimented on by Team Rocket to gain Pokémon - like abilities, or be transformed into a Pokémon - like being in a very creative and out - of - the - box fanfiction concept.
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.
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 possible motivation could be that she feels betrayed by her friends. Maybe she has a misunderstanding with Ash or the others, and Team Rocket takes advantage of this to convince her to join them.
If Team Rocket turns Ash into a Pokemon, it could lead to a really interesting story. Ash would have to experience the world from a Pokemon's perspective. He'd understand their struggles, like being caught and trained. This could also be a way for him to better understand his own Pokemon and their bond with him. And it would be a wild adventure as he tries to find a way to turn back to his human form.