You could write a fanfiction about a trainer who has lost their memory but still has an uncanny ability to battle with Pokemon. As they travel through the Johto region in Pokemon Gold, they gradually regain their memories through their interactions with Pokemon and other trainers. This could add an element of mystery and self - discovery to the story.
One idea could be exploring an alternate timeline where the main character makes different choices. For example, choosing a different starter Pokemon and how that changes their entire journey. Another could be focusing on the backstories of the Gym Leaders in the Pokemon Gold game, like what led them to become Gym Leaders.
A great plot idea might be a story where a new, mysterious Pokemon appears in the Johto region. This Pokemon has unique powers that disrupt the balance of the ecosystem. The protagonist has to figure out how to deal with this Pokemon, whether to catch it or find a way to send it back to where it came from. It could involve teaming up with other trainers and exploring uncharted areas of Johto.
One idea could be a crossover between the two generations. For example, a trainer from the Red era travels to the Gold region and has to adapt to the new Pokemon and different gym challenges there. Another could be exploring the backstories of some of the less - known Pokemon in both games. Maybe there's a hidden mystery about a certain Pokemon's evolution that a fanfiction could uncover.
One idea could be exploring an alternate timeline where the main character makes different choices in the game. For example, choosing a different starter Pokemon and how that changes their entire journey through the Johto region.
One idea could be a story about a trainer who discovers a rare and powerful Pokemon in the Johto region that is not typically found in the games. For example, a shiny, alpha form of a Pokemon like Totodile. The trainer then has to protect this Pokemon from a mysterious organization that wants to use it for evil purposes.
One idea could be a story where the protagonist's Pokemon from Pokemon Gold teams up with a Pokemon from Pokemon Crystal to face a new, powerful and mysterious threat that neither region has seen before. For example, a dark force that is causing natural disasters in both Johto and the Crystal region.
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.
Well, a cool plot for 'pokemon adventures gold and crystal fanfiction' could be centered around a time - traveling pokemon. This pokemon accidentally sends the main character back in time to when the Johto region was first being settled. The character then has to figure out how to get back while also dealing with the primitive pokemon training methods and different cultural views of pokemon. Or perhaps a plot where a powerful but cursed pokemon is found in the Crystal Cave. It curses those who try to catch it with bad luck, and the main character has to find a way to break the curse and catch the pokemon without getting too much bad luck himself. Also, a plot about a secret pokemon league tournament that only the best trainers in Johto are secretly invited to could be really exciting.
A plot idea could be to set the fanfic in an alternate Johto region where the roles of Pokemon types are reversed. Electric - type Pokemon are weak to Ground - type, but in this fanfic, it could be the other way around. The story could follow a trainer trying to adapt to these new rules while also uncovering a conspiracy behind this strange change. Also, you could explore the backstories of the Gym Leaders in a more detailed manner, like their childhoods and what led them to become Gym Leaders.
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.
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.