There could be a plot where they are both struggling with their identities in a different way. Since Jon is female, she might face different challenges in a male - dominated world of Westeros. And Daenerys, being with a female Jon, might have to deal with the reactions of her followers. Their relationship could be a way for them to support each other through these identity crises while also trying to claim the Iron Throne or bring peace to the Seven Kingdoms.
Some fanfictions might explore a scenario where they meet under different circumstances. For example, if Jon Snow was born a female and was sent to Essos instead of the Wall. Their first encounter there could lead to a whole new set of adventures and a unique relationship. This would involve exploring different cultures and power dynamics between them. It could be really interesting as they both have different leadership styles and goals, and seeing how they merge or conflict in a new context is exciting.
One possible plotline could be that their union brings about a new era of peace in Westeros. Their combined power and the love between them unites the warring factions. For example, Jon's connection to the North and Daenerys' powerful army and dragons could mean that together they are able to fend off any external threats. Another plotline might involve them facing opposition from some of the more traditionalist groups in Westeros who are against their relationship due to political or cultural reasons. This could lead to internal strife that they have to overcome together.
One interesting plotline could be their joint quest to defeat the Night King. They combine their forces, both the Unsullied and Dothraki with the Northmen. Their relationship also evolves during this time, from initial distrust to a deep mutual respect and perhaps something more romantic. They learn from each other's leadership styles and together become a formidable force against the undead threat.
Perhaps a plotline where they try to keep the pregnancy a secret at first. This could involve them hiding it from their allies and enemies alike. They might be worried about how the news would affect their standing in the various power struggles. Daenerys could fear that it makes her seem weak, while Jon might worry about the reaction of the Northern lords.
One interesting plotline could be their initial meeting being filled with suspicion but gradually turning into mutual respect as they realize they both have a common goal of saving the realm. For example, Jon might be initially wary of Daenerys and her dragons, but as they talk more, they find they can work together against the White Walkers.
One plot idea could be that in a world where their genders are swapped, they still have to face the same political challenges. Female Jon, with her Stark honor, and male Daenerys, with his Targaryen ambition, form an alliance that slowly turns into a romantic relationship as they realize they can achieve more together. Another could be a scenario where they meet in a different setting, away from the main events of the original series, and their relationship develops from there.
One interesting plotline could be them uniting the kingdoms without the bloodshed that occurred in the show. They might use their combined influence and the respect people have for them to bring about peace. For example, Jon's connection to the North and the wildlings, along with Daenerys' army and dragons, could be used to defend all of Westeros against a common enemy like the White Walkers that they both faced in different ways in the original story.
You can try searching on some well - known fanfiction websites like Archive of Our Own (AO3). It has a vast collection of fan - created works, and there's a good chance you'll find some stories featuring a female Jon Snow and male Daenerys there.
Many fanfics play with the idea of prophecy. Since both Jon and Daenerys have elements of prophecy surrounding them in the original story, fanfics can expand on this. For example, they might be the key to fulfilling a greater prophecy together that could save Westeros in a way that goes beyond just defeating the White Walkers. Their relationship can also be a catalyst for changes in the political and social structure of Westeros, with some fanfics delving deep into how they influence the different regions and houses.
Another great one is 'Frozen Fire'. Here, the story takes a different turn after the Battle of Winterfell. Daenerys and Jon, instead of the tragic end in the series, find a way to reconcile their differences. They start to build a new Westeros together, with their love for each other becoming a symbol of hope for the people. Their relationship is depicted as a force that can heal the war - torn land.
One interesting scenario could be their first encounter. Maybe Jon arrives at Daenerys' court as an envoy from the North. Their initial meeting would be filled with tension and curiosity. Jon, a man of the North, and Daenerys, the would - be queen with her dragons, would size each other up. Another scenario could be them fighting together against a common enemy, like the White Walkers. They would combine their forces, Jon with his knowledge of the North and Daenerys with her powerful dragons and army. And a third scenario might be a more personal one, where they gradually fall in love during their journey together, sharing their dreams and fears.