The premise of the show is that for the past 10,000 years, the Emperor of Mankind has been in living death and unable to guide his empire as it slowly crumbles away. If he were to suddenly one day regain the ability to speak, he would be very angry with the state of things and immediately start making massive changes, all while acting like a jerk the whole while.
The show draws heavily upon the previous lore of the 40k franchise, all while deconstructing it and poking fun at the many strange and bizarre stories that have cropped up along the way. All the while, the show also invents its own plot as the Emperor reunites with his sons and reforms mankind, though not without many pitfalls along the way. Characters from both the official canon, and those created for the show, appear throughout.
The series canon includes the BEHEMOTH Trilogy by Eliphas the Inheritor, and Chaos Descends by Karl the Deranged. There are also three spinoffs called "If The Emperor had a Podcast," an in-character podcast reviewing Black Library books, and BRO TRIP 40,000, staring the Primarchs Vulkan and Corvus Corax on a road trip across the galaxy.
Warning: The following section contains spoilers.
Custodes Captain-General Kitten has the Adeptus Mechanicus install a Text-To-Speech device onto the Golden Throne, allowing the Emperor to speak again. The Emperor immediately begins berating his subjects for ruining the Imperium, as what little he was able to perceive had greatly disappointed him. Kitten tells him of what has transpired since the Horus Heresy, including the Age of Apostasy, the arrival of the Tyranids, and the creation of the Inquisition. The Emperor's first decree is to disband the Ecclesiarchy and the Inquisition, which sets off a chain of events in the Inquisition attempting to purge Holy Terra of supposed heretics. The season ends as they are about to storm the Imperial Palace, after the Custodes claimed that the message was authentic.
Kitten successfully routs the Inquisition from the Imperial Palace, but Karamazov is spared for the moment. In the meantime, the Emperor's order for the Ultramarines to capture Magnus the Red turns out to be a success; while reluctant at first to reconcile with his father, Magnus is eventually convinced when the Emperor steals his soul back from Tzeentch. Karamzov returns to the palace with his army, but this time the Emperor convinces Karamazov that he is actually a fragment of his soul to feed his ego. While he is distracted, Magnus exiles the entire Inquisition into the Warp. The season ends with the return of Vulkan to his home planet of Nocturne, and the Emperor's Centurion reveals himself to be Rogal Dorn.
Rogal Dorn explains that he had taken a vow of silence to atone for his mistakes, but had to break that vow to keep Kitten from talking about Leman Russ in Magnus' presence. Magnus becomes enraged over his brother and starts destroying the throne room; in desperation, Kitten resigns as the Emperor's caretaker in exchange for the other Custodes help in calming Magnus. Afterwards, Magnus takes Kitten under his wing, and the two hatch a plan to independently save the Imperium and restore the Emperor. They travel to Nocturne, where they discover both Vulkan and Corvus Corax have returned; Corax in particular still hated Magnus and wanted him dead, and the two primarchs are now on their way to Terra.
Meanwhile, the exiled Inquisition meets up with Kaldor Draigo and Leman Russ in the Warp. Russ guides them to the Gate of Khaine to make their escape, but are caught by a massive daemon army. They are nearly slaughtered when suddenly, The Star Child bonds with Fyodor to become a living avatar of the Emperor, giving him the power to defeat the deamons and allowing the Inquisition to escape to Commoragh. Russ and the remaining forces of the Inquisition are taken to fight in the arena while the Fyodperor is taken to meet with Asdrubael Vect.
Kitten is sent by Magnus to Mars to look for the Proteus Protocol, which is in the possession of the Fabricator-General. Meanwhile, the Dark Angels, Cypher, and Eldrad's Harlequins are all traveling to Mars at the same time.
Spoilers end here.
When deciding what material to draw from in Warhammer 40,000 stories, Alfabusa has stated that "Everything is Canon... Except Malal." The series began before 8th edition when the storyline finally started moving forward after decades of stagnation; Alfabusa has stated that post 8th edition lore will be slowly worked into the storyline to fit into what he had originally planned.
The show is animated in Adobe After Effects and edited in Sony Vegas. Artwork used for the series is primarily sourced from official artwork used by Games Workshop, though some characters such as the Primarchs get special commissioned artwork specifically for the show. The music also draws from various official sources, primarily licensed Warhammer 40,000 videogames, but there are also original pieces created by Stringstorm for the show. Click here for a full Cast List, including voice actors, artists, musicians, etc.
Those who want to support the show can donate to Alfabusa's pateron.