The traitorous Primarchs or their descendants could also be antagonists. If they believe that the awakened Emperor will bring an end to their own power and influence, they would oppose him. For example, the Night Lords' successors might continue their ways of terror and oppose any attempt by the Emperor to bring order.
One possible plot twist could be that the Emperor awakens with a different ideology than expected. Maybe instead of immediately focusing on the destruction of his enemies, he decides to first reform the Imperium from within, causing chaos among the existing power structures.
The Primarchs could be main characters interacting with her. For example, if she had a vision for the future of the Imperium, she might consult with the more intelligent and far - seeing Primarchs like Guilliman. Another would be the Inquisitors. They are tasked with rooting out heresy and protecting the Imperium, so they could have important meetings with her to report on threats or seek her guidance. And of course, the Custodes. As her personal bodyguards, they would have constant interaction with her in many fanfiction scenarios.
The Akatsuki could still be a major antagonist. Even if Naruto is emperor, they might oppose his rule as it goes against their own goals of chaos and obtaining the tailed beasts.
A Vampire Lord from a long - lost dynasty could be a main character. He might be trying to reclaim his former glory in the 40k universe filled with so many powerful factions.
The Sith could still be antagonists. Even though Anakin has turned away from the dark side, there might be remnants of the Sith order who want to see his rule fail and plunge the galaxy back into chaos. They might try to manipulate events and turn Anakin's own people against him.
I think Warhammer 40k fanfics are a great way for fans to explore the vast and complex universe further. A good fanfic can add depth to the existing lore. For example, it might focus on the daily lives of the Imperial Guardsmen, which we don't often get to see in the official works. But there are also those that are just not up to par. Maybe they lack proper grammar or have a really convoluted plot that doesn't make sense in the context of the 40k universe.
Marneus Calgar is a well - known hero. He is the Chapter Master of the Ultramarines. Roboute Guilliman is also a major hero. He was one of the Primarchs and played a crucial role in the history of the Imperium.
One of the main characters is Ciaphas Cain. He is from the 'Gaunt's Ghosts' series. He is a bit of a reluctant hero, always getting into and out of trouble in the most interesting ways.
A specific Warhammer 40k fanfic could either be a masterpiece or a disaster. If it manages to capture the essence of the 40k universe, such as the scale of the battles, the complex politics between different factions, and the religious fanaticism that pervades the Imperium, it's likely to be a good one. However, if it goes against the established canon too much or has a poor writing style, it won't be as appealing.
The 'Warhammer 40k Son of the Emperor' fanfiction can be really interesting. It often explores the complex lore of the Warhammer 40k universe from a unique perspective. For example, it might delve into the character of the 'Son of the Emperor' and his relationship with the various factions in the universe. The fanfiction can also show how this character might influence the ongoing wars and power struggles. Some fanfictions in this genre are really well - written, with detailed descriptions of the dark and gritty Warhammer 40k setting.