Perhaps in the fanfiction, Fem Harry Potter is a descendant of an ancient Targaryen who was sent to the world of Harry Potter for safety. When she returns to the world of Westeros, she meets Rhaegar. They could bond over their shared sense of duty. Rhaegar might be intrigued by her different kind of magic and her unique perspective on the world, and together they could work towards a more just Westeros.
A possible plot could be that Fem Harry Potter is on a quest in a world that combines elements of both the Potterverse and Westeros. She encounters Rhaegar Targaryen who is also on a similar journey. They start off as rivals, each thinking the other is a threat to their goals. But as they face various challenges together, they come to respect and eventually fall in love with each other, and together they try to bring about positive change in this merged world.
A fanfiction could also be centered around a magical artifact that links the two universes. Rhaegar and Harry Potter both get drawn to this artifact. They must work together to unlock its secrets. Rhaegar's knowledge of ancient magic and Harry's experience with the Dark Arts could complement each other in this quest, all while dealing with the political intrigue in both their worlds.
They might have a love - hate relationship at first. Fem Harry Potter could be seen as an outsider by Rhaegar, and he might be suspicious of her magic. But as they get to know each other, the hate turns into love. Harry could be attracted to Rhaegar's noble and chivalrous nature, while Rhaegar could be drawn to Harry's strength and unique abilities.
In a Hufflepuff - Targaryen story, a Targaryen could be sorted into Hufflepuff. This would be an interesting contrast as Hufflepuffs are known for their loyalty and hard work, while Targaryens are often seen as more power - hungry. The Targaryen in Hufflepuff might have to learn to temper their desires for power and glory and instead focus on building strong, harmonious relationships within the house.
One possible plotline could be their first encounter. Maybe Rhaegar, with his noble and somewhat mysterious air, meets Fem Harry in a forest. Their initial meeting might be filled with confusion as they come from different worlds but are drawn to each other's unique qualities.
Rhaegar Targaryen is often depicted as a noble and chivalrous character. He is known for his good looks and his skill in combat and leadership. He has a certain air of mystery around him, which makes him all the more appealing.
One common theme is the clash of two different worlds. Harry comes from a world of magic with certain values and norms, while the Targaryen world in Westeros has its own set of complex politics and traditions. Their marriage often serves as a way to bridge these two worlds.
Perhaps Fem Harry Potter is mistaken for a Keyblade wielder at first. She has to prove herself in the Kingdom Hearts universe while also trying to find a way back to her own world. Along the way, she discovers that there are similarities between the magic in her world and the power of the Keyblades.
They could be allies in a fight against a common enemy. Suppose a dark force from Rhaegar's world and Voldemort team up. Harry and Rhaegar would need to combine their different magical abilities. Harry's ability to use a wand and Rhaegar's connection to dragon - related magic could be a powerful combination to defeat this new threat.
One popular piece might be 'The Targaryen's Bride' which delves into how fem Harry adjusts to the Targaryen court and her relationship with Rhaegar. It has a great build - up of their relationship, from initial encounters to falling in love.
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.