Perhaps a story about a Zorua that has the ability to see into the future in its dreams. It warns a group of trainers about an impending disaster that will affect the Pokemon world. The trainers, along with the Zorua and eventually a Zoroark, work together to prevent this disaster.
A more complex plot could involve a Zoroark using its illusions to protect a forest from humans who want to cut it down. The Zoroark disguises itself as various terrifying Pokemon to scare them away, but then a young girl befriends it and tries to find a way for the forest and the humans to co - exist.
One idea could be a story where a young trainer discovers a Zorua that has been separated from its pack. The trainer helps Zorua find its way back while facing challenges like wild Pokemon attacks and difficult terrains.
One plot idea could be that Ash discovers a Zoroark that has been separated from its pack. He decides to help it find its way back home while facing various obstacles along the way, like other Pokemon who are territorial. Another could be that a Zoroark, in its disguised form, befriends Ash without him knowing it's a Zoroark at first. Then when he discovers the truth, they have to work together to save a forest from a group of poachers.
Create a villain who is obsessed with capturing Zoroark for its powerful illusions. This villain could have a tragic backstory that makes them more complex. For example, they might have lost someone dear to them and believe that the Zoroark's illusions can bring that person back. They would stop at nothing to get what they want, which creates conflict in the fanfiction.
One idea could be that Ash catches Zoroark in a unique way. Maybe Zoroark is disguised as a Pokémon that Ash has been longing to catch for a long time. When Ash discovers the truth, instead of being angry, he is intrigued by Zoroark's intelligence and uses his own skills and the bond with his other Pokémon to earn Zoroark's trust and catch it.
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.
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.