Maybe the chosen one has to solve a mystery that threatens the Pokemon world. The Pokemon use their different types of skills like water - type Pokemon using their ability to explore underwater areas to find clues. Fire - type Pokemon can keep the chosen one warm in cold and dangerous places while they search for answers.
Another plot could be that the chosen one is from a different dimension and is unfamiliar with the Pokemon world. The Pokemon take it upon themselves to teach the chosen one about their world, its rules, and how to catch and train other Pokemon. This way, a bond is formed between them as they learn and grow together.
A third plot idea might be that Ash is the chosen one to bring peace between the different factions of legendary Pokemon. There could be some legendary Pokemon that are at odds with each other, and Ash, with his unique bond with Pokemon in general, is the only one who can bridge the gap. He would have to understand the reasons for their conflicts, which could be rooted in ancient history or disputes over territory. Along the way, he'd have to convince both sides that cooperation is better than conflict, and he might use his own experiences with his Pikachu and other Pokemon friends to show them how different species can get along.
Well, it depends on the specific fanfiction. Some might have a plot where the chosen one and their roommate embark on an epic Pokemon journey together, facing challenges and making new discoveries.
There could be a secret organization that believes the chosen one's power will disrupt the balance they have carefully maintained in the Pokemon world. They would be villains as they try to eliminate the chosen one and the Pokemon helping them, thinking they are doing what's best for the world but in a very wrong way.
One idea could be the main character being reborn as a Pikachu and having to navigate the world with its electric powers while making friends with other pokemon. Another could be being reborn as a Eevee and having the unique ability to evolve into any form at will, which causes both envy and admiration among other pokemon. Maybe the reborn pokemon has memories of being a human and uses that knowledge to outwit trainers and other threats.
A plot could revolve around a rookie XCOM soldier who has a special ability that catches the attention of all the Chosen. They each try to sway the soldier to their side, and the soldier has to navigate through their offers while remaining loyal to XCOM. Or perhaps a fanfiction set in a parallel universe where the roles of XCOM and the Chosen are reversed, and we see how the Chosen fight against an oppressive XCOM - like force.
The Chosen Undead could bring their unique skills, like the ability to wield powerful magic weapons, to the Harry Potter world. They might get involved in the fight against Voldemort, not because they care about the wizarding world's politics, but because they sense a similar kind of dark power in Voldemort that they've faced in their own world. Their presence could change the course of the battle in unexpected ways.
One plot idea could be a story where a trainer forms an unexpected bond with Reshiram. Maybe the trainer is initially afraid of Reshiram's power but over time they learn to work together and understand each other.
A plot idea could involve a Phantump that is actually a reincarnation of a human who had a strong bond with Pokemon. The Phantump then tries to find its way back to its human family while facing the challenges of being a Pokemon in a world that doesn't understand its true nature. It could be a heart - wrenching and exciting story.
One idea could be a crossover where Pokemon trainers visit the Avatar world. They could learn bending techniques and use their Pokemon in unique ways to help the Avatar in a great battle. For example, a Pikachu could use its electricity to enhance a waterbender's attack.
Maybe a story where a group of Pokemon in the Quest world start to develop their own language and culture. A trainer befriends them and tries to understand and document this new development, all while facing opposition from other trainers who think these Pokemon are strange and should be left alone.