One idea could be a story where a young trainer discovers a rare and powerful Pokemon in an unexpected place. Maybe in an old, abandoned mine. This Pokemon has unique powers that are different from what's known in the regular Pokemon world. It could be a Pokemon that can communicate telepathically with the trainer.
A plot could revolve around a group of trainers who come together for a special Pokemon tournament in the 'pokemon power of us' universe. But during the tournament, they discover a conspiracy to control the outcome. So, they have to work together, using their different Pokemon's powers, to expose the truth and ensure a fair competition.
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 team-up that no one expected. Like a villain and a hero from different universes having to work together in the Tournament of Power. They start off distrusting each other but gradually learn to respect and rely on one another. This could add a whole new layer of drama and character development to the fanfiction.
One idea could be exploring the origin of the 'power of darkness'. Maybe it was a forgotten magic that gets rediscovered by a young protagonist.
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.
A plot could revolve around a Pokemon RPG fanfiction where the main character is a Pokemon breeder who accidentally creates a new form of an existing Pokemon through a special breeding technique. This new form causes a stir in the Pokemon community, and the breeder has to deal with the consequences, like people trying to steal the Pokemon or Pokemon professors wanting to study it.
A more adventurous plot could involve an Audino that gets separated from its natural habitat and has to team up with a trainer to find its way back. Along the way, they face various challenges and encounter different Pokemon species, and the Audino discovers new strengths within itself. This plot could also explore the relationship between the Audino and the trainer as they grow closer during their journey.
One idea could be a story where a trainer discovers a Pokemon with a facade ability that allows it to change its appearance completely. This could lead to all sorts of misunderstandings and adventures as the trainer tries to figure out what's going on. For example, the Pokemon could pretend to be a rare and powerful species, attracting the attention of both good and bad trainers.
One idea could be a Pokemon trainer who gets bitten by a werewolf-like Pokemon and starts to take on werewolf - like traits. They then have to struggle with controlling their new powers while still trying to compete in Pokemon battles.
One idea could be a Pokemon that has the ability to transform into a mermaid and it goes on a journey to find its true origin. It could face challenges like being hunted by humans who want to study its unique form.