There are many talented authors in the fanfiction community. However, it's hard to single out the 'best' as it's subjective. Some authors who are quite well - known for their detailed and engaging stories might include [Author Name 1]. Their stories often have great character development. Another could be [Author Name 2] who is known for creating unique plotlines involving Khaleesi and her dragons.
One popular fanfiction might be about Khaleesi's journey in a different land with her dragons. In this story, she could face new challenges and form unexpected alliances. Another could be a story exploring the relationship between Khal Drogo and Khaleesi in more depth, perhaps showing their early days together in a more detailed way. And there are those that focus on the Mother of Dragons' rise to power, with her dragons playing crucial roles in battles and political maneuvers.
Daenerys is an obvious choice. Their relationship in the original series was complex and passionate, and in fanfiction, there are so many ways to explore it further. Another good character could be Ser Jorah Mormont. His loyalty to Daenerys and his knowledge of Westeros could create interesting dynamics with Khal Drogo. And perhaps the witch Mirri Maz Duur could also be paired with him in a fanfiction that delves into the more magical and vengeful aspects of the story, exploring what could have happened if their interactions had taken a different turn.
Khal Drogo's love story is quite tragic. He fell in love with Daenerys Targaryen. At first, their union was more of a political arrangement, but over time, true feelings grew between them. He was a powerful and fierce Dothraki khal. He gave Daenerys the power and confidence to grow. However, his life was cut short by a devious plot, which left Daenerys heartbroken and set her on a path of vengeance and her own rise to power.
The idea of motherhood is also prominent. Since she is the mother of dragons, fanfictions may explore her relationship with her 'children' in different ways. It could be a nurturing relationship, or one where she has to make tough decisions regarding her dragons for the greater good. There are also fanfictions that look at how her role as a mother affects her leadership and her perception among her followers.
You can start by looking on fanfiction websites like Archive of Our Own (AO3). It has a large collection of fanfics related to the Khaleesi and her dragons. Just search for 'Khaleesi Mother of Dragons' in the search bar, and you'll get a plethora of stories to choose from.
It might start with a way to connect the two universes. Maybe a magical portal transports Harry Potter to the world of Khaleesi. Then it would follow a plot that involves both the magical elements of Harry Potter and the political and power - based storylines of Khaleesi's world.
Jon Snow is also a very popular character in Khaleesi fanfiction. The idea of a relationship between him and Daenerys, whether it's romantic or a political alliance, is a common theme. Their combined claim to the Iron Throne and their different leadership styles make for interesting storylines.
There might be a fanfiction where Khaleesi uses her dragons in more creative ways. Like using them to communicate with the old gods of the North. This could lead to a whole new set of interactions and plot developments.
One common theme is his relationship with Daenerys. Many fanfictions explore how their love developed and how it changed both of them. Another theme is his leadership. Writers often delve into how he led his khalasar and the challenges he faced in that role.