Warhammer 40,000 is full of mysteries, some of which haven’t had answers since the original 40K “Rogue Trader” was first published over 30 years ago. In fact, very few elements of the 40K universe weren’t already mentioned at least in passing in the very first edition of the game and the supplementary material released in the first couple of years, including Tyranids and Genestealers. Very little has been retconned in fact, and even then there are still ‘in universe’ reasons for inconsistencies and changes. Of the playable races, only Necrons and Tau were added significantly after the fact, and even then the Necrons featured early on as the ‘chaos android’ in Space Crusade.
In real life, Games Workshop’s writers have created all kinds of little rabbit holes they can explore in future fiction, without necessarily knowing what the answers when the question is first posed. That the whole universe was setup in those first couple of years and is still only partially explored in detail now is a huge achievement when you think how rich and vast the universe is. 30 years later and we are finally getting some forward movement of the story reaching the end of the year 999.M41 but in that time plenty of mysteries unanswered, very few of which have been answered definitively. We’ve attempted to collate all the most significant mysteries together with the status of the answer here in one place.
If you know a mystery we have missed in our list, post in the comments below.
Who is the ‘large man in baroque power armour’ in Trazyn’s collection? Status: Theory. Although strongly hinted that this is one of the missing Primarchs, it could simply be any Space Marine or even an Inquisitor or other user of power armour such as a Rogue Trader. While if it was a Primarch that would be something Trazyn would value very highly and not want to let go of, it would seem odd that he turned up to help at the Fall of Cadia, but disappeared before they went and resurrected another Primarch. It is also suggested it may be Deathwatch member and Blood Angel Antor Delassio.
What is the Dawn Blade used by Farsight? Status: Theory. Since it’s almost certainly not a daemon weapon, the Dawn Blade is probably the last missing Crone sword of the Eldar, although it’s size is not consistent with that.
Who created the Tau and why, and what is the real aim of the Ethereals? Status: Theory. The Eldar, with the help of or using technology of the Old Ones, created the Tau possibly as a weapon to use against Chaos, given their negligible psychic potential. It may be that the Tau evolved naturally but that the Ethereals were genetically modified to allow Eldar or others to influence and speed up advancement of the Tau race.
What is in the Black Library and who or what is the guardian of it? Status: Unknown
Who created the Webway? Status: Answered. The Webway was created by the Old Ones and then adopted and extended and maintained by the Eldar, though their ability to maintain it was far reduced after The Fall. What was the original purpose of the Golden Throne and the secret project the Emperor was working on after he put Horus in charge of the Great Crusade? Status: Answered. The Emperor was attempting to create a gateway from Earth into the Webway, and technologies necessary to connect all of the Imperium to the Webway so that the Imperium could be run without needing to risk ships entering the Warp. It was the damage caused to this project by Magnus the Red attempting to psychically send a message to the Emperor to warn him of Horus’ treachery that ironically led to the Emperor sending Leman Russ to kill him.
Where are the missing Primarchs – Leman Russ, Vulkan, Corax, Jaghatai Khan and Rogal Dorn? Status: Unknown. Apart from knowing they disappeared, in most cases into the Eye of Terror, their current location and status is unknown, presumed dead, except Vulkan who may be unable to die due to his ability to reincarnate.
Where are the traitor Primarchs – Horus, Perturabo, Magnus the Red, Fulgrim, Lorgar, Alpharius, Angron, Konrad Curze, Mortarion. Status: Answered. Horus, Curze and Alpharius are dead (although Omegon may still be alive, or vice versa). The others are all daemon princes.
What purpose is served by the Pylons of Cadia, and who created those Pylons? Status: Mostly Answered. The Pylons were designed to constrain the Eye of Terror from further expansion and protect the surrounding systems from Warp storms. Cadia was not the only planet to have such Pylons, there were many others but Cadia seemed to be the nexus of the network, and with most of the other pylons destroyed, Cadia finally collapsed as the Cadian Pylons alone could not bear the strain of the full load. They were almost certainly created by the Necrons together with the C’Tan Void Dragon, although their original purpose might have been to simply cut off the galaxy from the Warp completely so as to cripple the psychic power of the Old Ones and Eldar.
Did Lion El’Jonsson or Luther, or both, turn to the side of Horus during the Heresy? Status: Unknown. Both are still alive or at least, in stasis, in The Rock.
Who is Cypher and what is his plan? Status: Unknown. Cypher wishes to get to earth, and this he has achieved with the help of Roboute Guilliman. But what happens next seems to be a mystery. It may be he wishes to kill the Emperor, perhaps to raise the Emperor to Godhood, or perhaps because Cypher is evil after all. Or perhaps he simply wishes to provide evidence confirming what really happened between the Lion and Luthor on Caliban during the Horus Heresy, to clear the name of one or the other.
What is the sleeping dragon on Mars and is it a C’tan? Status: Theory It is very strongly hinted that the Emperor defeated a dragon on ancient earth (leading to legends like St. George and the Dragon) and it is said that he then imprisoned it deep on Mars where it sleeps in the Noctis Labyrinth, which Necrons have recently attempted to enter. There is also a C’Tan known as the Void Dragon, and the source of the Necrons’ most advanced technology. It is therefore strongly hinted that these are one and the same.
Who or what is the Sanguinor? Status: Theory. The Sanguinor may be a ‘living saint’ like Saint Celestine, kept in limbo in the Warp except when summoned by the Emperor when needed. While rumours say he is Azkaellon, he may instead be the original Sanguinor, the Herald of Sanguinius, created as a proxy when Sanguinius was the emperor of the Imperium Secundus
How has Mephiston been able to overcome the Black Rage? Status: Unknown.
What became of Alpharius and Omegon, and which side were they really on during the Horus Heresy? Status: Unknown. At least one of them might be dead. They may or may not have been on the same side or on opposing sides in the Heresy. They may or may not have joined the Heresy deliberately to help or to hinder Horus or to ensure a particular outcome such as the death of the Emperor that would actually turn out to be more desirable. They at least seemed to be involved with the Cabal, a group of humans and aliens trying to manipulate things behind the scenes, and were probably aware of what would happen to the Emperor should he die.
Who is Janus, founder of the Grey Knights? Status: Theory. Janus is probably one of the agents of Malcador the Sigillite, a loyalist member of a traitor legion. However since Janus was an ancient god with two faces, it is suggested that Alpharius might have become Janus.
What happened to the two missing legions and their Primarchs? Status: Theory. Probably the biggest mystery of all and one we may never get an answer to because the in real life answer was to create free ‘slots’ for players to invent their own, the strongest suggestions are that both failed the Emperor in some way and were sanctioned, most likely by being killed by Leman Russ and the Space Wolves, who is referred to as the Emperor’s Executioner. That makes it extremely likely that at least one of the two was killed in this way if not both. Malcador the Sigillite is also illustrated sitting on a throne with two skulls on the armrests, numbered with the two missing Primarchs’ numbers. However, there is also occasional suggestion that while one was killed, the other was sent on a secret mission from which there could be no return. The wilder theories about this suggest that Primarch became Sigmar of the Warhammer Fantasy world, which at least once upon a time was said to be a world surrounded by Warp Storms and cut off from the rest of the galaxy. A variation of that theory says that Vulkan is Sigmar, and the Stormcast are Perpetual soldiers he has created from his own geneseed.
What happened to the Squats? Status: Answered. It’s often said that The Squats were retconned out of existence, but there is an in-universe answer – they were eaten by the Tyranids. Even if they weren’t, while they don’t have a range of miniatures, who’s to say they don’t still exist as one of the many abhuman races. The Demiurg may or may not be the refugees from that event, or they may be a new and different alien race instead. Where is Lion El’Jonsson? Status: Answered. The Lion is held in stasis at the core of The Rock, while Luther remains alive but insane, also in The Rock’s inner prison cells. Is Roboute Guilliman really healing? Status: Answered. He may or may not have been partially healing in stasis, though most likely is that was just wishful thinking. He certainly was still near death when Cawl and Yvraine removed him from stasis, and it required both Eldar magic and special armour to resurrect him – probably the Eldar magic allowed his soul to be held in place and his armour keeps his body functioning almost like a portable Golden Throne. Who or what is Saint Celestine? Status: Answered. As a Living Saint, she is kept in a form of stasis in limbo in the Warp until summoned by the Emperor. Where did the Legion of the Damned come from? Status: Answered. They may be the souls of many dead Space Marines, but it is strongly suggested they are specifically the Fire Hawks chapter were lost in the warp where they now remain trapped, effectively with the same ‘living saint’ as Saint Celestine or The Sanguinor. Just enough wiggle room is given that this may be only part of the answer, especially as the Fire Hawks did not disappear until after first sightings of the LotD, however they are also suggested to be able to time travel somewhat due to the vagaries of the Warp.
What will happen to the Emperor’s power if his body dies? Status: Theory. Various factions, notably within the Inquisition, have competing theories. Some believe he will die completely, others that he may return to life (that he is a Perpetual), and others that he will ascend to Godhood. But since no one seems to know for sure there’s no way to find out.
Who is the Primogenitor of the Blood Ravens chapter? Status: Theory. It is strongly suggested that the Blood Ravens are descended from loyalist refugees of the Thousand Sons, specifically a company that used Raven iconography. This would explain their psychic powers, thirst for knowledge and propensity to turn to Chaos.
Who controls the Black Ships? Status: Answered. This is answered in Master of Mankind if not also in other places, the Black Ships that collect psykers for use in the Astronomicon or for training as sanctioned psykers are run by the Sisters of Silence.