A great plot could involve a time - travel aspect. The protagonist is sent back to the time when Pokemon Yellow was first set, and they have to use their knowledge of modern Pokemon training and battling to change the course of history in the Pokemon world. They might also meet the original trainers from the game in a different way and form new alliances.
Another plot idea is a story centered around a Pikachu that refuses to evolve. It has its own reasons for not wanting to become a Raichu, perhaps it has a special bond with a certain type of Pokemon that can only be maintained as a Pikachu. The main character has to support the Pikachu in its decision while facing opposition from other trainers who think evolution is always the best path.
Perhaps a fanfiction where the main character discovers a time - traveling device in the Pokemon world. They travel back to the very beginning of the Pokemon Red and Yellow era and have to prevent an event that would change the future of the Pokemon world in a bad way. Along the way, they meet the original Professor Oak as a young man and help him with his early Pokemon research.
One idea could be a story where the main character discovers a new, rare Pokemon in an unexpected place, like in a hidden cave in Viridian Forest. Another could be a fanfiction where the Pokemon trainers from Red and Yellow team up to face a new, powerful villain who has a unique ability to control Pokemon in a different way than the usual villains in the games. Maybe also a story about a trainer's Pokemon evolving in a very different way due to some strange phenomenon in the Kanto region.
One idea could be to focus on a new trainer's journey in the world of Pokemon Yellow. They could start with a Pikachu that has a unique ability not found in the original game.
A cool plot could be that Lance, in the Pokemon Yellow world, decides to start a new type of Pokemon training school. He recruits the protagonist from the game as his first student. Together, they develop new training techniques and discover new Pokemon evolutions. But an old rival of Lance hears about this and tries to sabotage their efforts. So they have to not only deal with the challenges of training and discovery but also fend off this rival who is jealous of Lance's new project.
One idea could be a story where Red and Yellow have to team up with their Pokemon to stop a new and powerful villain who is stealing rare Pokemon. Another could be a story about their journey to discover a hidden Pokemon species that is said to have special powers. And they could also face challenges like a natural disaster in the Pokemon world and have to use their skills and Pokemon to survive.
One idea could be a story where the main character is a Pokemon trainer who discovers a rare and powerful Pokemon that no one has ever seen before. They then have to protect it from evil organizations who want to use it for their own gain.
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.
One idea could be a story where Peridot tries to prove her worth to Yellow Diamond in a non - traditional way. Maybe she discovers a new form of energy on Earth that could benefit the Diamond Authority, and she has to convince Yellow Diamond to give her a chance to explore it further.
An interesting plot for a Pokemon Conquest fanfiction could be a tale of a trainer who loses their memory but still has an innate connection with their Pokemon. As they journey through the kingdoms, they slowly start to regain their memories through their Pokemon battles and interactions. Another plot could involve a forbidden love between trainers from rival kingdoms, and how they try to keep their relationship a secret while also dealing with the pressures of their kingdoms' expectations. You could also create a fanfiction where a new type of Pokemon emerges, and all the kingdoms are vying to be the first to tame and control it, leading to a series of intense battles and political intrigue.
One idea could be exploring an alternate universe where the protagonist starts with a rare and unique Pokémon that's not available as a starter in the original game. Another could be a story about a Pokémon trainer who has the ability to communicate with Pokémon in a more in - depth way than normal, and how that changes their journey in the Unova region. Maybe a fanfiction about a group of Pokémon trainers coming together to solve a mystery that threatens the balance of the Unova region.