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.
Ash's character would be forced to adapt in many ways. His usual positive and enthusiastic attitude might be dampened as he gets involved with Team Rocket. He would have to hide his true feelings and intentions, which could make him seem more reserved and calculating. This is a big change from his usually open - hearted self. Misty, being the strong - willed character she is, would start to take on a leadership role. She would be the one constantly reminding Ash of their true purpose and trying to find a way out. Her relationship with Ash would also change, becoming more of a partnership where they both rely on each other's strengths to survive in the Team Rocket 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, 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.
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.
Pikachu would probably be very confused at first. It's used to fighting against Team Rocket, not being on their side. It might resist and try to zap Ash to snap him out of it.
It would also have an impact on the other villainous teams in the Pokémon world. They might see Ash joining Team Rocket as a sign that they can also recruit more powerful trainers. This could lead to more alliances between the bad guys and more complex plots to steal Pokémon and cause trouble all around the Pokémon 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.
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.
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.
Some of his more loyal Pokemon might try to resist the change. For example, Pikachu could use electric shocks to try and jolt Ash back to his senses. Pikachu has a strong bond with Ash and would be very confused and sad about his decision to join Team Rocket.