His other Pokemon like Charizard might outright refuse to follow Ash if he joins Team Rocket. Charizard has a strong sense of pride and loyalty, and joining the bad guys goes against everything it stands for. It could lead to some epic battles between Ash and his disobedient Pokemon.
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.
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.
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.
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.
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.
Well, it could make for a really interesting fanfiction. Dawn joining Team Rocket would change the whole dynamic. Her Pokémon might not be too happy about it at first. She could bring new ideas to Team Rocket, since she has a different way of thinking compared to Jessie, James and Meowth. However, it's also possible that she would secretly be working against Team Rocket from the inside, trying to take them down while pretending to be one of them.
He might become more cautious. Usually, Ash is quite bold and rushes into things. But if he's in a Team Rocket - centered fanfiction, he'd likely be more careful as he's constantly surrounded by danger. For example, he'd think twice before challenging a new Pokemon or entering an unknown area.
The Pokémon League might condemn Ash's actions. Despite Team Rocket's wrongdoings, killing is not an acceptable solution in the Pokémon world which values friendship and co - existence. Ash could face consequences such as being banned from Pokémon battles or certain areas. On the other hand, some trainers who have been harassed by Team Rocket for a long time might secretly support Ash.
One thing that would happen is that his Pokémon battles would take on a whole new meaning. Instead of battling for the sake of becoming a Pokémon master, he might be battling to further Team Rocket's goals. His Pokémon would have to adjust to this new purpose. Also, Ash would probably have to wear Team Rocket's uniform, which would be a really strange sight for fans who are used to seeing him in his normal get - up.
It would likely bring a new level of harmony (literally) to Ash's team. Since Meloetta has musical powers, it could use its melodies to boost the morale of the other Pokémon on the team. For example, before a big battle, Meloetta could sing a song that makes Pikachu feel more energetic and ready to fight.
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.