Maybe there's a story where Flygon gets injured and Sountland has to find a special herb to heal it. Along the way, Sountland faces many challenges and has to use its wits and strength. The story could focus on their friendship growing through this difficult time.
A more complex plot could involve a mysterious force that is causing Pokemon in the area to act strangely. Flygon and Sountland are the only ones who seem immune. They set out on a journey to discover the source of this force. Along the journey, they meet other Pokemon who either help or hinder them, and they have to figure out who to trust. As they get closer to the truth, they realize that it's something much bigger than they expected and they must use all their combined skills to stop it.
Their abilities can be combined in a rescue mission. For example, if there are Pokemon trapped in a cave. Sountland can sniff out the exact location of the trapped Pokemon from outside the cave. Flygon can then use its digging ability (if we assume it has some) along with its flying to enter the cave from above and clear the way for the rescue. This would show how their different abilities work together for a common goal.
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.
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.
One idea could be a story about a young trainer whose family has a long - forgotten pokemon heritage. Maybe they discover an old family pokemon that was thought to be lost, and they embark on a journey to learn about its powers and how it was related to their ancestors. Another plot could involve a pokemon family feud, where two branches of a family have different ideas on how to train and care for their pokemon, leading to conflicts and challenges.