Team Rocket could always be the main antagonists. They might have a new and more devious plan to steal Ash's Pikachu and other rare Pokemon that Ash and Brock encounter on their journey.
Maybe a fanfic where Ash and Brock discover a hidden Pokemon village that is in danger from a powerful, evil Pokemon. They must use their skills and the help of the village Pokemon to defeat the threat. This could involve Brock using his knowledge of Pokemon care to heal the injured village Pokemon, while Ash strategizes for the battle.
The fanfiction might focus on their journey. Red, being a well - known trainer, and Yellow, with her own special abilities, could be on a quest to discover new Pokemon or solve some mystery in the Pokemon universe. It may also show how their partnership evolves over time, from just acquaintances to really good friends or something more.
The main character is likely to be the Pokemon trainer. In the context of 'pokemon adventures yellow and red fanfic', it could be a young boy or girl who starts their journey in the Kanto region, just like in the original games. They would be the ones catching and training Pokemon.
The protagonist of Pokemon Yellow is an obvious potential ally. They are on their own journey to become a Pokemon master and could easily team up with Lance. Another could be Professor Oak. He has a vast knowledge of Pokemon and could provide valuable information and resources to Lance. Also, the Gym Leaders in the Pokemon Yellow world could be allies. They are all skilled trainers in their own right and could join forces with Lance when facing a common threat, like an evil team trying to disrupt the Pokemon League.
They would become even closer. The shared responsibility of having a baby would strengthen their bond. Eddie would be more protective of Venom, and Venom would be more gentle towards Eddie, knowing they are in this together for the sake of their future child.
One common theme is Misty's growth as a character. In Pokemon Red and Yellow, she starts as a somewhat headstrong and feisty trainer. Fanfics often explore how she matures over time. Another theme could be her relationships, especially with the protagonist. It might show how they develop a deeper friendship or something more romantic. Also, adventures in the Pokemon world are a big part of it. Fanfic authors might create new quests or challenges for Misty and the gang, building on the original game's world.
Gary Oak is also popular. He can be portrayed as a more complex character in fanfiction. Maybe a story where he teams up with Ash against a greater threat, or a plot where we see his own personal growth and struggles as a Pokemon trainer in the context of the Yellow and Red games.
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.