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 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.
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.
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.
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.
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.
One reason could be its loyalty to Team Rocket. In many Pokemon stories, Team Rocket is the bad guy group. So, if Meowth is part of Team Rocket in the fanfic, when they do something really bad like trying to steal a rare and beloved Pokemon from a village, the villagers might catch Meowth and punish it instead of the whole team. They could make it do hard labor, like carrying heavy sacks of Pokemon food around the village all day long. This is because Meowth is more accessible and less intimidating compared to the other members of Team Rocket.
In a fanfic about Meowth evolving, it could be that a powerful enemy forces Meowth to adapt and evolve in order to protect its friends. This evolution might give it new abilities and a different appearance, perhaps more intimidating to foes.
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.