40K is a setting that runs on mysteries. GW deliberately leaves things unanswered because the speculation is half the fun. The lore is structured so that contradictory accounts exist for almost everything, narrators are unreliable, and Imperial records have been rewritten so many times that even the characters in-universe don’t know what’s true. It’s a feature that rewards obsessive reading and punishes anyone looking for clean answers.
Here are some of the questions the community can’t stop arguing about. I’ve got opinions on all of them, and I’m sure you’ll disagree with at least half.
The Missing Primarchs
Two of the Emperor’s twenty sons were completely erased from history. Legions II and XI. Nobody will say what happened. The other Primarchs refuse to discuss it. Every theory (rebellion, genetic failure, xenos contamination, deliberate sacrifice) is plausible and none are confirmed. This is probably the most debated question in all of 40K lore, and I think GW is smart enough to never answer it definitively.
What makes this mystery work so well is how the other Primarchs react when it comes up. In the Horus Heresy novels, Dorn goes cold. Guilliman changes the subject. There’s a moment where Horus uses the Lost Primarchs as leverage against Fulgrim, implying he knows what happened, and the weight of that scene only works because we don’t. The community has essentially split into camps: the “they rebelled and were destroyed” camp, the “genetic catastrophe” camp, and the increasingly popular “they were sacrificed to seal something in the Warp” camp. I lean toward something involving a deal with xenos that went wrong, but that’s pure speculation. The point is that every theory feels possible, and GW has been extraordinarily disciplined about not letting anything slip in forty years of publishing.
The Void Dragon
There’s a C’tan shard (fragment of an ancient star god) imprisoned beneath the surface of Mars. Some lore strongly implies that the Void Dragon is the entity the Adeptus Mechanicus has been worshipping as the Machine God for ten thousand years. If true, the entire theological basis of the Mechanicus is a lie built on an alien prison. This has never been confirmed or denied. It just sits there in the lore, being incredibly suspicious.
The evidence is compelling. The Dragon of Mars in the novel Mechanicum is explicitly a C’tan, and its imprisonment predates the founding of the Mechanicus by millennia. The Mechanicus has always had an inexplicable affinity for technology that borders on psychic communion, and the Void Dragon’s domain is mastery over the material and the mechanical. The implication is that the entire Cult Mechanicus, every forge world, every tech-priest, every sacred ritual of machine maintenance, is powered by the unconscious psychic emanation of a trapped alien god that doesn’t even know it’s being worshipped.
If GW ever confirms this, it would crack the Imperium in half. The Mechanicus would face an existential crisis that makes the Horus Heresy look like a disagreement. I think that’s exactly why they’ll never fully confirm it. It’s more useful as a lurking dread than a resolved plot point.
What Are Tyranids Running From?
The Tyranids came from outside the galaxy. The question nobody has answered: why? Were they attracted by the Astronomican? Or are they fleeing something in the intergalactic void that’s even worse than they are? GW has dropped hints about this without ever committing to an answer, and the implications of “something scarier than the Tyranids” are genuinely terrifying.
The Astronomican theory is the most commonly cited explanation, and it makes a kind of sense. The Emperor’s psychic lighthouse is the brightest signal in the galaxy, and a species that navigates by psychic resonance would naturally be drawn to it. But that doesn’t explain the urgency. Hive fleets don’t behave like they’re exploring. They behave like they’re consuming everything in their path as fast as possible, as if they need the biomass now. The “running from something” theory suggests that the Tyranids already stripped their home galaxy clean and whatever was left is something they couldn’t eat. I lose sleep over what that might be.
The Emperor’s True Nature
Is the Emperor a collective psychic entity born from ancient shamans? A Perpetual? A weapon made by the Old Ones? Something else entirely? The lore gives different answers depending on the source. I think the ambiguity is intentional. A fully explained Emperor is a less interesting Emperor.
The shaman origin story was the original explanation from early editions: thousands of prehistoric psykers collectively reincarnated as a single being of immense power. The Perpetual angle, introduced in the Horus Heresy novels, frames him as an immortal who has lived since ancient Anatolia and guided humanity from the shadows for tens of thousands of years. But even the characters closest to him can’t agree on what he is. Malcador the Sigillite, his oldest friend, sometimes speaks about him as if he’s a man who accumulated too much power. The Custodes speak about him like a god. The Primarchs each saw something different when they looked at him, which might be the most telling detail of all. He shows people what they need to see. That’s not a human trait. That’s something else.
Where Are the Missing Primarchs?
Not the Lost two (II and XI). The ones who disappeared after the Heresy. Russ walked into the Eye of Terror. The Khan vanished into the Webway. Vulkan is a Perpetual who’s somewhere. Corax entered the Warp and may have transformed into something inhuman. Dorn’s body was never found. Each disappearance is a future storyline waiting to happen, and GW has started cashing in (the Lion returned recently, Guilliman is back). Who’s next is one of the community’s favorite guessing games.
My money’s on the Khan being next. His disappearance into the Webway is the most narratively convenient for a return, especially with the Dark Eldar and Harlequin factions needing more lore attention. A Khan who’s been fighting through the Webway for ten thousand years, possibly changed by the experience, possibly allied with or hunted by the Drukhari, writes itself. Russ is the fan favorite pick, but I think GW is going to make us wait on that one because the Space Wolves fanbase is the loudest and GW knows anticipation sells more books than resolution.
The Rangdan Xenocides
This one doesn’t get as much mainstream attention, but it should. Early in the Great Crusade, the Imperium fought a series of wars against an alien species called the Rangdan. These wars were so devastating that they nearly destroyed the Imperium before it was fully established. Multiple Legions were deployed. Casualties were catastrophic. The details have been almost entirely suppressed in Imperial records.
What makes this interesting is the timing. The Rangdan Xenocides overlap with the period when the two Lost Legions were erased. Some fans have connected the dots and theorized that one or both of the missing Primarchs were lost during the Rangdan wars, either killed, corrupted, or compromised in some way that required a total records purge. The Rangdan themselves are described in fragments as a parasitic species capable of subverting other organisms. The implication that a Primarch might have been subverted by an alien parasite is the kind of horror that 40K does best.
The Hrud and the Entropy Plague
This is one of the deep-cut mysteries that most lore discussions skip, and I think it deserves more attention. The Hrud are a xenos species that the Imperium has encountered repeatedly but never fully understood. What makes them genuinely terrifying isn’t their technology or their numbers. It’s their relationship with time. The Hrud generate an entropy field, an area of accelerated temporal decay around their migrations. Everything near a Hrud migration ages at catastrophic speed. Soldiers sent to fight them come back as old men. Equipment rusts and crumbles within hours. Fortifications that took decades to build disintegrate in days.
During the Great Crusade, the Iron Warriors fought a campaign against a massive Hrud migration, and the casualties weren’t from combat in any traditional sense. Perturabo watched his legionaries age to death in front of him. Tanks corroded to nothing. An entire expeditionary fleet’s worth of equipment was rendered useless. The campaign broke something in Perturabo’s already fragile psyche and is considered one of the factors that pushed him toward the Heresy. But here’s the mystery: nobody knows how the Hrud do this. It’s not Warp-based, or at least not Warp-based in any way the Imperium recognizes. The Hrud don’t appear to be psykers. They don’t worship Chaos. Their entropy effect seems to be a fundamental property of their biology, as if they exist slightly out of phase with normal time and their presence drags surrounding matter forward through its own decay cycle. The Imperium has never developed a countermeasure because they’ve never understood the mechanism. And the Hrud are still out there, migrating through the galaxy in vast swarms, aging everything they pass through to dust. That a species this dangerous has been essentially filed under “miscellaneous xenos threat” tells you something uncomfortable about how many problems the Imperium is simply too overwhelmed to properly address.
What’s in the Imperial Webway?
The Emperor’s greatest project wasn’t the Space Marines or the Golden Throne. It was the Imperial Webway, a human-accessible section of the Eldar’s interdimensional highway network. He was building a gate beneath the Imperial Palace that would have given humanity access to faster-than-light travel without relying on the Warp. Magnus the Red accidentally destroyed the project’s psychic wards when he tried to warn the Emperor about Horus’s betrayal, and daemons poured through the breach.
But here’s the thing: the project wasn’t just a doorway. The Emperor had been building something in the Webway. Sections of a human city. Infrastructure. The start of a civilization that would exist entirely outside the Warp’s influence. What happened to all of that after the breach? Is it still there, overrun with daemons? Has something else moved in? The Custodes fought a war in the Webway tunnels for years during the Heresy, and the descriptions of what they encountered down there get progressively more nightmarish. Some of the things they fought weren’t daemons at all but something native to the Webway itself. That section of the lore is deeply underexplored and I want someone at Black Library to write a full novel about it.
The Cacodominus
In M34, a single alien psyker called the Cacodominus had psychically dominated thirteen hundred planetary systems. When the Imperium finally killed it, the psychic death-scream was so powerful that it burned out every astropath within several sectors and caused ships in the Warp to lose navigation, resulting in the loss of entire fleets. Billions died in the aftermath. And this was just one creature.
The lore doesn’t tell us what species the Cacodominus was. It doesn’t tell us if there are more. It doesn’t explain how one being could dominate over a thousand systems without anyone noticing until it was too late. It’s a single paragraph in a timeline entry, and it implies that there are threats in the 40K universe that make the major factions look like regional problems. The community occasionally brings this up and the conversation always ends with “well, that’s terrifying” and nothing else. I think about it more than is probably healthy.
These mysteries are features, not bugs. A universe where everything is explained is a universe with nothing left to discover. The community debates around these topics are some of the best content in the fandom. Reddit threads about the Lost Primarchs regularly hit thousands of comments. YouTube creators have built entire channels around speculative lore analysis. The arguments never get resolved, and that’s the point. 40K’s refusal to give clean answers is what’s kept fans arguing for almost forty years, and I hope GW never stops.
For a deeper dive into these topics, check out our full mysteries article.
