A possible plot could involve Sapphire and Ruby getting separated from Steven during a dangerous adventure. They then have to rely on their unique powers and their love for each other and Steven to find their way back to him. Along the way, they might encounter new gems that challenge their relationship and their loyalty to Steven.
One plot idea could be that Sapphire and Ruby are having a disagreement about how to best protect Steven. Sapphire, with her future vision, sees a potential threat approaching in a very different way than Ruby does. This leads to some tension between them as they try to figure out the best course of action for Steven's safety.
Maybe there could be a plot where Steven accidentally uses his powers in a way that affects Sapphire and Ruby's relationship. For example, he might create a situation where they start to see different aspects of their relationship that they hadn't considered before. This causes them to reevaluate their bond and how they interact with each other and with Steven.
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.
In the fanfiction, Ruby and Sapphire could be having trouble adjusting to life in a new town. Steven, who has experience with change, could introduce them to new friends and show them all the fun things about the place. Meanwhile, they could teach Steven more about their unique Gem culture, like how they fuse and their special powers. This would create a story full of cultural exchange and friendship building.
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.
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.
To develop their relationship, you could explore their past. Maybe there were times when they first fused into Garnet and had doubts about each other. By delving into these memories and how they overcame them, it can strengthen their relationship in the fanfic. Also, having them face new challenges together, like dealing with a new type of gem enemy, and seeing how they support each other through it.
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.
Love is a very common theme. Their relationship is often explored in-depth, from the early days of their meeting to their deep, abiding love as Garnet. Another theme is loyalty. They are always there for each other, and this loyalty is highlighted in many fanfictions. For example, in stories where they face challenges together, their loyalty to each other never wavers.
One idea could be exploring a new mega evolution for a less - known Pokemon in the Hoenn region. For example, making Linoone have a mega evolution with a unique design and new abilities. Another plot could revolve around a trainer who discovers a hidden, ancient Pokemon that was thought to be extinct in the Hoenn caves. This could lead to a race among different trainers and teams to either protect or capture it.
One idea could be that May and Steven go on an adventure to discover a new type of Pokémon that has some connection to Steven's knowledge of stones. They could face various challenges together, like difficult terrains and other Pokémon trainers who are also after this special Pokémon.
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.