A third idea is that the reader is a Pokemon trainer who has lost their memory. They wake up in a Pokemon center with no recollection of who they are or what their Pokemon are. With the help of the Pokemon center nurse and their own Pokemon, like a Pidgey, they start to piece together their past. As they travel around to different places looking for clues, they encounter various challenges and make new friends, both human and Pokemon.
Another plot could be that the human has a special ability that allows them to enter the dreams of pokemon. In these dreams, they learn about the pokemon's past, their hopes, and fears. This knowledge helps the human to better understand pokemon in general and they use this understanding to improve the relationship between humans and pokemon in their world. Maybe they even discover a conspiracy that is affecting the pokemon in their sleep, and they have to stop it.
One plot idea could be that the male reader is a new trainer starting out in a region that has been affected by a strange phenomenon that is making Pokemon act out of character. He has to figure out what's causing it and stop it while building his own team of Pokemon. Another idea is that the male reader discovers a hidden Pokemon species that is thought to be extinct and has to protect it from poachers.
Well, for a Pokemon and reader fanfic, you could have a plot where the reader is from our world but wakes up in the Pokemon world with amnesia. As they explore, they gradually remember their past life while also forming a team of misfit Pokemon. Or perhaps a story where the reader is a scientist who is researching a new type of Pokemon evolution and ends up having an adventure with the Pokemon they are studying. There could also be a fanfic where the reader is a Pokemon breeder who stumbles upon a unique Pokemon egg and the journey of hatching and raising the Pokemon from it.
Another plot could be that the reader is lost in a strange part of the Pokemon world and Pikachu is the one who finds them and leads them to safety. Along the way, they become great friends and share many adventures. This could involve exploring new areas, meeting different Pokemon species, and learning about the secrets of the Pokemon world.
A really interesting plot could be that the reader is a paranormal investigator who has come to Derry to study the strange disappearances. They end up encountering Pennywise, but instead of being a victim, the reader uses their knowledge of the supernatural to communicate with Pennywise. The two form an unlikely alliance to uncover a deeper mystery in Derry that is related to Pennywise's origin, and during this process, their relationship evolves in unexpected ways.
One idea could be focusing on a trainer who is trying to reunite the two legendary Pokemon of Ruby and Sapphire, Groudon and Kyogre, to stop a greater threat that emerges when their power imbalance causes natural disasters. The trainer has to travel across both Hoenn regions, facing challenges from different gym leaders who have different views on how to handle the situation.
A plot could revolve around a Pokemon contest that is only for water - type Pokemon. Misty, being a water - type expert, helps May train her Pokemon for this special contest. Along the way, they face challenges and learn more about each other's training styles.
Perhaps a fanfic where Red and Green are transported to an alternate dimension where the rules of Pokemon battles are completely different. They have to quickly adapt and figure out how to get back home. In this dimension, Pokemon have new and strange abilities, and Red and Green's bond is tested as they try different approaches to deal with the situation. Their combined experience with Pokemon in their own world becomes a valuable asset as they explore this new and dangerous place.
A great plot could involve a Pokemon that has the ability to travel between the Emerald and Ruby regions at will, causing chaos as it steals rare items. The fanfic could follow the journey of two trainers, one from each region, as they try to track down this Pokemon and return the items. They start off as rivals but gradually learn to work together. The different landscapes and Pokemon of the two regions would add a lot of variety to the story.
One idea could be that N and Touya team up to discover a new, rare Pokemon species in a hidden, untouched region. They face various challenges along the way, like dealing with a powerful and territorial Pokemon that guards the area. This could lead to them bonding and learning more about each other's views on Pokemon and the world.