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.
The Empress herself is of course a main character. Often, you'll also find Space Marines, as they are a significant part of the Warhammer 40k universe and interact with the Empress in various ways. Imperial Guardsmen may also be present, depending on the plot of the fanfiction.
I don't know for sure, but it could be the Space Marines. They are often central characters in Warhammer 40k stories.
One of the main influences on the origin of the Warhammer 40k story is classic science - fiction. Works like 'Dune' might have inspired the complex political and power - struggle aspects within the Imperium of Man. Also, traditional fantasy elements, such as the concept of noble warriors (like the Space Marines being a sort of 'knights in space') were an influence.
In the Warhammer 40k War of Secrets novel, it's possible that there are main characters from different factions. There might be a tech - priest from the Adeptus Mechanicus who is trying to unlock some technological secrets. Or perhaps a Commissar who is involved in uncovering some political secrets within the Imperium. There could also be a Chaos cultist whose actions drive part of the story as the Imperium tries to root them out.
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.
In many of the novels, Asdrubael Vect is a significant character. He is a powerful and cunning leader within the Dark Eldar society.
In 'The Knight of Talassar', Sir Hekhtur is a main character. He is a noble and skilled Imperial Knight who has to face various challenges. His character is well - developed, and we see his growth throughout the story.
Azrael is a main character. He is the Supreme Grand Master of the Dark Angels and plays a crucial role in leading the chapter.
Marshal Helbrecht is a main character. He is a powerful and respected leader within the Black Templars. His decisions often shape the course of their crusades.