If Jon meets Rhaegar, it could change the story drastically. For one, Jon might gain a new understanding of his Targaryen heritage. He could learn secrets about his family that were lost over time. This new knowledge could influence his decisions regarding the Iron Throne and his relationships with other characters.
One possible plot could be that Jon, after learning his true identity, travels back in time and meets Rhaegar. Rhaegar could see the potential in Jon and start training him in the ways of leadership and combat. This would be a great way to explore their relationship and how Rhaegar's influence might shape Jon's future decisions.
Their relationship could develop into a very strong father - son bond. Rhaegar, having lost so much, could pour all his hopes and dreams into Jon. Jon, on the other hand, could look up to Rhaegar as the father he never had. They might travel together, facing various challenges and growing closer through shared experiences, like fighting off enemies or dealing with political intrigue in Westeros.
One possible scenario could be that Rhaegar recognizes Jon Snow as his son immediately. He might be filled with a mix of emotions, pride and regret perhaps. He could then start to train Jon in the ways of the Targaryens, sharing secrets about their family's past and the power of dragons.
Another option is Fanfiction.net. Although it has a different layout and community compared to AO3, it still has a large number of fanfictions. Try searching with specific keywords related to the story you want, like the names of the characters and the theme of love. Just be aware that the quality can vary widely.
The unique pairing is one aspect. Rhaegar, a complex and tragic character from the ASOIAF universe, and Fem Jon, which is a different take on the well - known Jon Snow character, create an interesting dynamic. Their love story can explore different power dynamics, family legacies, and the whole concept of fate within the context of the fictional world.
At first, they might be at odds. Rhaegar may initially view Fem Jon Snow as a threat to the Targaryen legacy, while she sees him as part of the old regime. But as they get to know each other better, they realize they have common goals, like protecting the realm from the impending threats. This could lead to a deep bond, perhaps even a romantic one. They would support each other in their respective quests, with Rhaegar using his knowledge and influence, and Fem Jon Snow her unique skills and perspective from the North.
A plot could involve Fem Jon Snow being trained in the ways of the dragon by Rhaegar's spirit. Since Rhaegar was known for his connection to dragons, he could guide her to discover her own dormant dragon - riding abilities. This could lead to her uniting the remaining Targaryen forces and reclaiming the Iron Throne. Or perhaps they meet in a dreamscape where Rhaegar reveals the true purpose of her existence, which is to bring peace between the North and the Targaryen - ruled South.
There could also be other supporting characters that play important roles in the fanfiction. For instance, Tyrion Lannister might be there to act as an advisor to Daenerys during her encounter with Jon. His wit and political acumen could influence how the meeting between Jon and Daenerys unfolds.
Well, in many fanfictions, after Jon meets Daenerys, they might face challenges from external enemies or internal politics. Maybe they have to unite different factions to survive. Or, their relationship could face tests due to their different backgrounds and goals.