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There are many of them from secret identities to what lives under what planet and even include things like mars: home to just robots, or sleeping place of a intact c'tan. What's your favorite and please go into details and debate the posible.

Just a minor correction, the void dragon rumored to be on Mars is just a shard, not intact. We know the void dragon got splintered because there is a story in the most recent codex about one of its shards that escaped imprisonment.

My personal favorite mystery is whether or not Trazyn the infinite has a primarch in his collection. The 5th edition codex describes a giant man clad in baroque power armor in the vaults of Solemnace, and a later white dwarf article implied that this might be Vulcan.

Gotta say my favorite mystery is the origins of the tyranids. Did they really run out of food, and have only just begun to arrive, or are they running from some greater threat? Rather ominous either way

Why legions II and XI were expunged from all imperial records, and what those legions were like when they were around.

Will Russ/Vulkan ever return to their chapters?

where is marbo

Did the High Lords of Terra actually have the capability to revive the Emperor the moment he was placed on the Golden Throne and yet withheld treatment to come into more power themselves? I remember reading that somewhere in an early edition of 40k.

 oldzoggy wrote:
where is marbo

Hunting down Cypher, naturally.

What are the Altansar Craftworld Eldar hiding under their helmets? Why do they only speak in whispers?

How did the Mandrakes come to be, and what is Kheradruakh trying to summon with his skull pile?

What REALLY happened with the Cursed Founding?

Cypher. Is he the key to saving the Imperium, or just a Fallen Angel running around causing shenanigans?

The purpose and relationship between Ordo Necros, Ordo Vigilus, and Ordo Desolatus.

What in the name of all you may or may not hold holy happens when the Emperor kicks the bucket... is the imperium lost, does he come back as before as the eternal being he is, will he be a warp entity, will he come back but mad and broken from the warp

The mystery of the box that the Grey Knights has that potentially could destroy/save mankind, and why does it have a symbol on it that's only found on the Golden Throne.

The mystery of the Omega Machine or whatever that the Deathwatch has, and what's in the central room.

I think the two are linked, and could go on forever about this theory, but I won't.

Also, what is Orikan/what is his goal?
Same goes for the Silent King.

Who made the Tau?

What happened to the Ordo Time or whatever the hell they were called?

Is Earth and Holy Terra the same planet? There seems to be a discrepancy between their positions on modern and 40k star charts respectively.

 TheCustomLime wrote:
Is Earth and Holy Terra the same planet? There seems to be a discrepancy between their positions on modern and 40k star charts respectively.

Oh, that's always been like that. Earth is supposed to be Holy Terra, it's just situated somewhere else for some reason. Probably on purpose since it's sci-fi/fantasy. Real Earth is pretty far out on the edge; not the greatest location for the center of power.

Edit: Whoops, its the mysteries thread, time for bed lol. But there are a lot of mentions of real places (Himalayas and such) so it'd be pretty weird if it was a different planet.

There is the one mystery that has kept me up for many-a-night. How do Space Marines go to the bathroom in that armor of theirs?

 War Kitten wrote:
There is the one mystery that has kept me up for many-a-night. How do Space Marines go to the bathroom in that armor of theirs?

Duh. Internal toilet

Cypher's agenda and the fate of Dark Angels

On the back of what TheManWithNoPlan said:

What exactly happened to the Legions (and for the love of the Emperor, don't say 'Ultramarines' haha)?

And what happened to their Primarchs and all their relics (e.g. the weapon(s) and armour of the Primarchs)?

It's heavily inferred at least - but are the Legion of the Damned the Emperor's demons/angels?

Da Mediokre Painta wrote:
It's heavily inferred at least - but are the Legion of the Damned the Emperor's demons/angels?

In the past, the LotD were thought to be confirmed as the mutated/warped forms of the Fire Hawks chapter. However, the LotD dataslate offers six different theories, of which the Fire Hawks and warp entities of the Emperor are only two such possibilities. Others included the gestalt consciousness of all of humanity itself manifested from the warp and marines in the throes of traveling backwards through time acting upon set missions. However none of these theories are given greater value over another.

I appreciate this return to a more nebulous answer rather than the old confirmations.

jareddm wrote:

Da Mediokre Painta wrote:
It's heavily inferred at least - but are the Legion of the Damned the Emperor's demons/angels?

In the past, the LotD were thought to be confirmed as the mutated/warped forms of the Fire Hawks chapter. However, the LotD dataslate offers six different theories, of which the Fire Hawks and warp entities of the Emperor are only two such possibilities. Others included the gestalt consciousness of all of humanity itself manifested from the warp and marines in the throes of traveling backwards through time acting upon set missions. However none of these theories are given greater value over another.

I appreciate this return to a more nebulous answer rather than the old confirmations.

I like it too. The Fire Hawks answer needed WAAAY to many coincidences to take place to work.

 Drogga wrote:
Gotta say my favorite mystery is the origins of the tyranids. Did they really run out of food, and have only just begun to arrive, or are they running from some greater threat? Rather ominous either way

This. A thousand times this. The sheer scale of the possible "WTF" is scurry as gak.

Who/What are the watchers in the dark, and what is happening with The Lion? Accounts range from him being almost dead and possibly slowly healing to being ready to go but just in stasis.

 EngulfedObject wrote:

 TheCustomLime wrote:
Is Earth and Holy Terra the same planet? There seems to be a discrepancy between their positions on modern and 40k star charts respectively.

Oh, that's always been like that. Earth is supposed to be Holy Terra, it's just situated somewhere else for some reason. Probably on purpose since it's sci-fi/fantasy. Real Earth is pretty far out on the edge; not the greatest location for the center of power.

Edit: Whoops, its the mysteries thread, time for bed lol. But there are a lot of mentions of real places (Himalayas and such) so it'd be pretty weird if it was a different planet.

Terra is earth. It is in the same place in the galaxy. Sat on the lower clockwise edge of a minor arm between the Perseus and Sagittarius arms.

The difference in star charts is down to 38000 years having passed. The maps show Terra as being at about 9 o'clock where as earth is normaly shown at 12, presumably due to the movement of the galaxy in that time. It has always been the case that only part of the galaxy is controlled by the IOM, due to Terra being in the west.

Mysteries, well... Farsight has a few that could be jimmied out of the closet.

The Harlequins + Tau relationship. This was a really fun mystery incorporated in Xenology and the Fire Warrior book that the Harlequins and Cegorarch instigated the accelerated evolution of the Tau and the Warp Storm around the system. It made a lot of sense for the Harlequins to have their own agenda and the Tau to have a part to play in their plan, i wish they would revisit this.

Similarly I like the idea that the Laughing God is just the racial memory of the Deciever worshiped until he became a separate Warp Entity. This would explain the supposed link between them.

Hm.. when is Mina coming back, and what the hell happened to Sabrina?!

Otto Weston wrote:Did the High Lords of Terra actually have the capability to revive the Emperor the moment he was placed on the Golden Throne and yet withheld treatment to come into more power themselves? I remember reading that somewhere in an early edition of 40k.

It's from the Inquisitor rulebook.

War Kitten wrote:There is the one mystery that has kept me up for many-a-night. How do Space Marines go to the bathroom in that armor of theirs?

One word: Intubation.

ALEXisAWESOME wrote:The Harlequins + Tau relationship. This was a really fun mystery incorporated in Xenology and the Fire Warrior book that the Harlequins and Cegorarch instigated the accelerated evolution of the Tau and the Warp Storm around the system. It made a lot of sense for the Harlequins to have their own agenda and the Tau to have a part to play in their plan, i wish they would revisit this.

Xenology just suggested Eldar, and Fire Warrior never mentioned them... and it's just as or more likely to be Necrons, given the cultural similarities.

Similarly I like the idea that the Laughing God is just the racial memory of the Deciever worshiped until he became a separate Warp Entity. This would explain the supposed link between them.

This one I like.

Who/what are the "Tau" Ethereals? What's their purpose and motives?

What is Khaine's Gate and what's going to happen with it? What does Vect know about it?

Cypher, the surviving primarchs, Sanguinor, Grey Knight founders.

@Furyou Miko

Forgive me for not dredging up the exact quote, but the Tau codex said when the Etherals came there were ''Strange Lights up in the mountains'', in the Fire Warrior book this is expanded upon to say ''Lithe, slender brightly garbed figures capered through the mists''. While i know Craftworlders can be brightly garbed, and all Eldar would appear graceful to a Tau, the exact wording seems to point directly to Harlequins.

And it makes a lot of sense doesn't it? If T'au had a large functioning webway gate, the Dark Eldar would of raided them to extinction in their infancy. So it makes sense for the Harlequins to be the only faction who know of and can use the small Webway portals on/near T'au.

 ALEXisAWESOME wrote:
Forgive me for not dredging up the exact quote, but the Tau codex said when the Etherals came there were ''Strange Lights up in the mountains'', in the Fire Warrior book this is expanded upon to say ''Lithe, slender brightly garbed figures capered through the mists''. While i know Craftworlders can be brightly garbed, and all Eldar would appear graceful to a Tau, the exact wording seems to point directly to Harlequins.

Very interesting. Now I see where the fan theories are coming from. Oddly enough, I think I actually read this in the codex a long time ago and forgot about it.

 Furyou Miko wrote:
Xenology just suggested Eldar, and Fire Warrior never mentioned them... and it's just as or more likely to be Necrons, given the cultural similarities.

Cultural similarities such as...?