I'm not entirely sure as it depends on the specific fanfiction. But it might involve Naruto having some sort of connection to Homura, perhaps in an alternate universe where Naruto's lineage is related to Homura in unexpected ways.
Another theme is the exploration of different powers. Naruto has his ninja techniques and Homura has her own unique abilities. Fanfictions often play around with how these powers interact, like if they could combine their powers to create a new and powerful technique.
They could start by being suspicious of each other. For example, Homura might think Naruto is a threat to her mission (if she has one in the Naruto world) with his powerful jutsu. Naruto could be confused by Homura's strange technology and time - stopping powers. But then, as they see each other's determination, they start to respect one another and communicate. Maybe Homura helps Naruto by using her time - stop to give him an advantage in a fight, and Naruto in return protects Homura from some of the more dangerous ninja in his world.
Obviously Naruto would be one of the main characters. And if he's the son of Homura, then Homura would also be a key character. There might also be the usual Naruto characters like Sasuke and Sakura who would be involved in the story in some way.
One interesting story could be about Naruto and Homura teaming up on a special mission. They might use their unique skills, Naruto with his ninja techniques and Homura with her own abilities, to overcome various challenges and enemies along the way.
Another idea is that Homura somehow gets trapped in the Naruto universe during one of her time - loop attempts. Naruto discovers her and is intrigued by her strange powers. Homura, on the other hand, is determined to find a way back to her own world while also getting involved in Naruto's journey to become Hokage. They could exchange knowledge about their respective worlds, like Homura teaching Naruto about time manipulation on a small scale and Naruto showing Homura the power of chakra.
One popular Naruto Homura fanfiction is 'The Bond of Fire and Shadow'. It delves into an alternate universe where Homura has a unique connection with Naruto and they face various challenges together. The story is known for its well - developed characters and exciting plot twists.
A good fanfiction starts with a strong concept. For Naruto and Homura, it could be something like 'What if they had to swap powers for a day?' Build on this idea by creating interesting scenarios. Develop their relationship gradually. Don't rush into making them best friends or lovers right away. Let the story unfold naturally, with twists and turns to keep the readers engaged.
Sayaka and Homura have a complex relationship in the 'Puella Magi Madoka Magica' series. In fanfiction, their relationship can be explored in various ways. Some fanfictions might focus on their friendship, perhaps delving deeper into how they could support each other through the tough battles and the emotional turmoil they experience in the original story. For example, a fanfiction could show how Homura's time - traveling abilities could be used to save Sayaka from making some of the more tragic choices she made in the anime.
The theme of resistance is also seen. Since the Puella Magi world can be quite harsh, a male Homura might resist the system in different ways. He could use his male perspective to find loopholes or form alliances that a female Homura might not have considered. This can add a new layer of complexity and intrigue to the fanfiction stories.