For a Pokemon Special Red and Yellow fanfiction, a cool plot could be that a strange illness starts affecting Pokemon in the region. Red and Yellow suspect that it has something to do with an ancient curse. They then embark on a quest to find the source of the curse. Along the way, they have to battle trainers who are trying to stop them because they believe the curse is a natural way of controlling the Pokemon population. Red and Yellow have to convince them otherwise and also find a cure for the sick Pokemon.
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.
A plot idea could involve Red and Yellow getting transported to a different dimension in the Pokemon world. In this dimension, the rules of Pokemon battles are different, and they have to quickly adapt. Maybe they find that their usual strategies don't work and they need to form new bonds with their Pokemon to figure out how to get back home. They might also meet alternate versions of their friends and enemies there.
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.
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 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.
Fanfiction about Pokemon Special Yellow and Red often explores unique storylines. It might focus on the relationships between the characters in the games. For example, the bond between the Trainer and their Pokemon could be delved into more deeply, showing how they grow together.
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.
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.
Well, a plot could involve Red going back to the starting regions to relive his early days, but this time with a twist. He might find that the Pokemon he once caught have developed in unexpected ways, or there could be a mystery about some strange occurrences in the areas he first explored. It could also be about Red training a new, inexperienced trainer, passing on his wisdom.
One common theme is friendship. Just like in the original Pokemon concept, the friendship between the Trainer and their Pokemon is often emphasized. It can be shown through how they support each other in tough situations.
One idea could be a story where the protagonist discovers a hidden, powerful Pokemon in an uncharted area of the Kanto region. This Pokemon could have unique abilities that change the way battles are fought in the game's world.