It could be Giovanni. If Giovanni gives an order that Meowth finds completely unacceptable, like harming innocent Pokemon for no good reason. Meowth, having a soft heart deep down, might not be able to go along with it and thus betray Team Rocket.
One reason could be unrequited love. In the Pokemon world, Meowth has a soft spot for certain Pokemon, like the Skitty. If in a fanfiction, Skitty rejected Meowth's advances, it would make him sad. Another could be his longing for acceptance. Meowth is a part of Team Rocket, but often they don't fully appreciate his skills. He might feel sad and underappreciated in a fanfiction scenario. Also, memories of his past life on the streets, before joining Team Rocket, might haunt him and bring about sadness.
There's also a chance that an old enemy from Ash's past resurfaces. This enemy, who has a long - standing grudge against Ash, could find a way to use Ash's Pokemon to get revenge. They might have developed new techniques or powers over time that allow them to influence the Pokemon's loyalty.
Well, one possibility could be that Meowth betrays Team Rocket. Maybe he gets tired of their constant failures and decides to side with Ash and his friends. He might see that they have a more positive and successful approach to their Pokemon journey.
However, over time, he could develop resilience. The experience of being abandoned might force him to become stronger, both physically and emotionally. He may learn to trust again, but it would be a slow process as he has to overcome the initial emotional trauma of abandonment.
One possibility could be that Meowth evolves after a deep emotional experience. Maybe it befriends a Pokémon that is in great danger and through the process of saving it, Meowth unlocks a new level of power within itself and evolves. This could lead to a whole new form with different abilities and a more noble appearance.
Meowth joining Ash in a fanfiction could also lead to some interesting character development for both. Ash might learn more about the Pokémon world from Meowth's perspective, especially the seedy side that Meowth has been a part of with Team Rocket. And Meowth could learn about friendship and loyalty in a new way, different from what he's experienced with Jessie and James.
A writer can use Meowth's body language. For example, they can describe his drooping ears, his slow and slouched walk, and his tail hanging low. This physical appearance immediately gives the readers an idea of his sadness. Also, the use of simple dialogue like 'Meowth meow (I'm so sad)' can be effective.
In such a fanfiction, perhaps Ash betrays his friends for power. He might be lured by an evil organization with the promise of rare Pokémon or ultimate power, and in the process, turns his back on Pikachu and the others.
Well, perhaps there could be a fanfiction where a powerful and mysterious Pokemon trainer captures both Meowth and Pikachu. The trainer forces them to battle each other for his amusement. But instead of fighting, they team up to escape. They use their unique skills, like Meowth's ability to speak human language to communicate with other Pokemon that can help them, and Pikachu's electric attacks to break through barriers. During their escape, they learn more about the trainer's dark secrets and also become closer friends.
In a fanfic, Meowth's evolution might be a result of a magical spell gone wrong. Instead of evolving into a normal form, it becomes a hybrid of different Pokemon types. This new form gives it strange and wonderful abilities, like being able to turn invisible or create illusions. But it also has to deal with the confusion of its new identity and how other Pokemon and humans react to it.