Well, you could do a fanfic where the protagonist is a Pokemon ranger in the Ruby universe. They are assigned to protect a particular area that is home to a lot of unique Pokemon. But then an illegal poaching ring starts to target those Pokemon. The ranger has to use their skills and the help of their own Pokemon to stop them. Another plot could be about a young trainer who enters a Pokemon contest in Hoenn. They face a lot of challenges and learn new strategies along the way. Also, a fanfic about a trainer who finds a mysterious egg in Ruby's world and has to take care of it until it hatches into a very special Pokemon would be interesting.
One idea could be to focus on a trainer who discovers a rare and powerful Pokemon in an unexpected part of the Hoenn region. Maybe a Pokemon that was thought to be extinct. Another could be a fanfic where the main character has to stop an evil team from misusing a powerful ancient artifact in Ruby's world. Or perhaps a story about a Pokemon trainer who befriends a Pokemon that has trouble evolving and they go on a journey to find a special way to make it evolve.
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 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.
A really interesting plot for a Pokemon Ruby and Sapphire fanfiction could be set in an alternate Hoenn region. In this version, the roles of certain Pokemon types are reversed. For example, Water - type Pokemon are rare and Electric - type Pokemon are the dominant force in water - based areas. The main character could be a trainer who has to adapt to these new rules. They might have to find creative ways to battle and train their Pokemon. This could lead to some really unique and exciting adventures, as they encounter different challenges and make new friends and enemies along the way.
One idea could be exploring an alternate universe where the starters of Ruby and Sapphire have different evolutions. Another could be a story focused on a side character from the manga, like giving a backstory to a Gym Trainer. Maybe also a story where the legendary Pokemon Groudon and Kyogre form an unexpected alliance instead of their usual rivalry.
One idea could be a story where the characters from Pokemon Gold and Pokemon Ruby team up to stop a new, powerful villain who is trying to control all the Legendary Pokemon. They could travel through both regions, facing different challenges along the way.
One idea could be to focus on a new trainer in the Ruby Scar region who discovers a rare and powerful Pokemon that has been lost for centuries. This Pokemon could hold the key to an ancient mystery that the trainer then sets out to solve.
A great fanfic idea could be that Wally gets lost in an uncharted area of the Pokemon Ruby world. He has to rely on his wits and the help of his Pokemon to find his way back. During this time, he might discover a new type of Pokemon or a unique item that gives him an edge in battles later on.
Perhaps a fanfic could be about a Pokémon from Ruby and Sapphire that gets lost in a different region. The Pokémon has to find its way back home while making new friends and facing challenges in the unfamiliar environment. Along the way, it could encounter different trainers and Pokémon species, and the story could show how it adapts and overcomes obstacles to return to Hoenn.
One idea could be Ruby facing a new type of Grimm that has unique abilities, like the ability to manipulate time in a small area. This would put Ruby in a tough situation where she has to figure out how to combat it while being affected by the time distortion. Another plot could involve Ruby getting lost in a Grimm - infested area and having to rely on her wits and the little resources she has to survive and find her way back to her team.
Perhaps the story could explore how Ruby's pregnancy affects her relationships with her team members. Some might be overly protective, while others could struggle to accept the change in her situation. It could also be interesting to see how her pregnancy impacts her relationship with her weapon and combat abilities.