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.
Perhaps a new, original villain. A dark ninja from a long - lost clan who has discovered the secrets of battle avatars and wants to use Naruto's Asura power to complete a dark ritual that would give him ultimate control over the ninja world. This villain could have his own set of powerful battle avatar abilities and minions, making him a formidable foe for Naruto.
Well, it could be about Naruto somehow getting the power of Asura and having to face off against a powerful enemy in a battle avatar form. Maybe he has to protect the Hidden Leaf from a new threat that only his newfound power can defeat.
It could be Orochimaru. He might have learned about the Avatar's unique power and wants to use it for his own dark experiments. So he tries to break Naruto's seal to get to the Avatar. He would be a great villain as he's always after powerful things and doesn't care about the consequences.
Kaguya could be a great antagonist. Even though she was defeated in the main Naruto story, she could be resurrected or have some lingering influence. Her power - hungry nature and her desire to control everything could put her at odds with Indra and Asura, who are symbols of two different paths in the ninja world. She might try to manipulate them to further her own goals or eliminate them as threats to her reign.
Starscream could also be a main villain in this fanfic. He is always looking for a chance to gain power and prove himself. He might see the battle of Autobot City as an opportunity to take over the Decepticons or get some valuable Autobot technology for his own gain.
Maybe an ancient evil spirit that has been awakened due to some mistake. It targets Ageha because she has a pure and powerful chakra. Naruto, being the hero he is, tries to fight the spirit, but he quickly realizes that he needs Ageha's help as well as the help of all his friends to defeat this powerful foe.
The main villain could be Darkseid. Imagine if he somehow finds a way to enter the Naruto universe. He would be a formidable foe for both Naruto and Supergirl. His omega beams and immense strength would be a huge challenge for them to overcome.
It could be a rogue ninja from the village with the Tenshikage. Maybe he's jealous of the Tenshikage's power and wants to take it for himself. He could be causing chaos in the village, stealing important ninja scrolls and attacking innocent villagers.
A new character could be introduced as the main villain. This character could be someone from an ancient clan that was once in control of the 10 - tailed beast but lost it. Now, seeing Naruto with that power, they want it back and will stop at nothing to get it. They could have unique powers and abilities that make them a formidable foe for Naruto and his friends.
It could be a new character, a powerful dark wizard who wants to use the combined power of Naruto's chakra and Pikachu's electricity for his own evil purposes. He creates all sorts of dark creatures and sends them after Naruto and Pikachu to try and capture them. He's very cunning and has a lot of minions to do his bidding.
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.