A new character could be created as the main character. Maybe an orphan who discovers they have the Rinnegan avatar powers. This character would have to learn about both the Naruto and Avatar worlds from scratch, making their journey of self - discovery and power - mastering more exciting as they interact with characters from both universes.
Sasuke could be a great main character. He already has the Rinnegan in the Naruto series. Imagine him in the Avatar world, using his Rinnegan - enhanced skills to learn about the elements and become an avatar - like figure, but with his own dark and brooding personality.
The Sage of Six Paths himself could be the key character. Since the Rinnegan was originally his power, he could appear in the fanfic in some form, like a spirit or a time - traveling version of himself. He could then directly bestow the Rinnegan upon Naruto, seeing Naruto's potential and the need for such power to maintain the balance in the ninja world.
It could be Sasuke. Since he already has the Sharingan and later acquires the Rinnegan, he has a natural connection to both powerful eyes. A story could focus on his further adventures and how he uses the combined powers of the eyes in different situations.
Naruto could also be the main character in such a fanfic. Even though he doesn't have the Rinnegan in the original, in a fan - created story, he could be involved in a plot where he has to deal with the secrets of the Rinnegan. For example, he might be trying to help a friend who has the Rinnegan and is in danger because of its secrets.
Sasuke could also be the main character. Given his connection to powerful eyes in the Naruto series, if the Rinnegan was abandoned, Sasuke's role would change significantly. He would have to re - evaluate his own power and place in the ninja world, which could make for a really interesting story with him as the main focus.
It could be an unknown Uchiha who was overlooked in the main story. Maybe they were born with the Rinnegan but due to some political unrest in their village, they were forced to hide their power and were thus neglected. In the fanfiction, they could come out of hiding and shock everyone with their Rinnegan - based abilities.
Obviously Naruto would be one of the main characters as the title implies he's the emperor. Another could be Sasuke. He might be Naruto's right - hand man or sometimes a rival within the new empire. From the Avatar world, Aang could be a major character. He could either be an ally or someone who initially doubts Naruto's rule but later comes to respect him.
It could be an ancient dark ninja who wants to use Naruto's new 'avatar of death' powers for his own evil purposes. This ninja might have been researching death - related jutsus for years and sees Naruto as the key to his ultimate power.
Madara Uchiha could also be the main character in this type of fanfiction. Although in the original story his actions are mostly related to his grand plans for the Ninja world, in a fanfiction, it could be explored what would happen if he decided to leave Konoha specifically because of his Rinnegan and the power it holds.
One idea could be a story where the character with the Rinnegan avatar has to navigate a world where the rules of chakra and bending are combined. For example, they might use the Rinnegan's powers to control different elements in a way similar to how avatars control them in the Avatar world.
It could be Orochimaru. He's always been interested in power and with Naruto having the Asura power in this fanfic, Orochimaru might see it as a great opportunity to steal that power for himself and use it to create an even more powerful battle avatar.