ALRIGHT.
So this is meant to clear up the endless confusion surrounding Mimir's world, specifically the origin and purpose of Kul Elna... Or, as he calls it, 'Elna'am'.
IF YOU ARE READING THE FANFIC AND DO NOT WANT TO BE SPOILED ON FUTURE EVENTS, DO NOT CLICK THIS!
The first thing you should know is that the world Mimir is from, in general, attempts to 'flawlessly' (that word alone is flawed...) meld the manga arcs to the anime- this includes Doma. However, it does this in a way that tries to make a SMALL bit more sense concerning Doma's seeming origins of duel monster 'monsters'.
And this ties into the stories that the 'Dragon' Mimir spoke with would always tell him. Those stories? Legends passed down for years from ATLANTIS.
The 'lineage' and 'timing' goes like this. 10,000 years BCE, in other words 'cave times', a group of humans strike a deal between themselves and shadows, as requested from the creator- 'Light'. The deal is that one protects the others in their realm, and as such, the shadows are more inclinded to side with their mother as opposed to their father, 'Darkness'. With the aid of the shadows and Light, a civilization begins to grow and flourish at an alarming rate- this civilization is 'Atlantis' and its empire...
But Darkness isn't too pleased with this. Tainting three of the most powerful shadows he can find (as Darkness represents Death and destruction and can therefore not 'truly' create anything), he creates what become known to Mimir's people as 'the three things', 'Ziz', 'Bahamut', and 'Leviathan'. Each has a purpose, an order of attack, and each strike Atlantis in their own way.
'Bahamut' moves first despite being meant to move last however- at this time, Darkness has yet to realize that the three have an order at all in fact. As something that feeds and gains strength from vengeance and rage, he has difficulty against the seemingly peaceful and utterly loyal-bound people of Atlantis- as such, the people seal him away, only for him to speak this prophecy;
'As I fall by your blood, so shall I rise- as your blood becomes mine so shall all that I see.' The prophecies are further recorded by one of what was many seers at that time, and are recorded into a thick tome, never to be consulted again.
Following Bahamut comes 'Ziz', the 'Shapechanger'. As a being that feeds on fear he was meant to move first, and as he makes his attack it becomes apparent why. He easily gains the power needed to challenge Light herself, and in the end she is forced to divide herself into three altering beings, so as the three that Ziz divides into can no longer match her power. These three pieces are from then on called the nameless, the 'Evil Gods', and are sealed within the three pieces of Light, the pieces in turn sealed within powerful 'stones'.
These stones are to be passed down for generations by the Atlanteans descendants, but getting to that later...
Following Light's 'destruction' and the sealing of Ziz, the ruler of Atlantis comes to find himself and his people turning to an alternate form of sustainability and power. Leviathan, operating on envy and despair, does so- and as he feeds off the mourning people who have lost relatives, forms the stone 'Orichalcos'...
Soon entrapping all of Atlantis in its power. All is not lost however, even as the entire empire is brought down with little to no evidence of existing- the three Knights, who have resisted the power thus far, challenge Leviathan as he arises for the final strike with his new set of pawns and warriors. However, realizing they have little they can do against the serpent being, they turn their focuses to evacuation- they manage to carry a 'small' number of the people to the African continent using the shadows bound to them (dragons, hint hint), before turning to defend them from Leviathan itself.
The end result is sealing him away at the cost of their own bodies, shadow and light both- their draconic forms become as stone, forming large cliffs in the middle of next to nothing on Egypt's soil.
Time passes. Cultures come and go- early on, those who would become the Egyptians meet with the Atlantean survivors and defend them from some unknown threat, or at least do so before the Atlaneans themselves can use the powers still available to them. As a gift, the 'three stones' are presented to the Capital at the time- but this, along with many other meetings and histories, quickly fade into obscurity.
Closer to Mimir's time, 'Elna'am' as it's called becomes a safe haven for thieves and tomb robbers alike. It becomes a place where they can trade freely, and even live, and as a result a sort of 'outer ring' to the village's core begins to develop. This 'ring', combined with the cliffs and catacombs of the village itself prove a sturdy defense against any attempts to attack the new villagers for their crimes, particularly with an entrance that only allows one person at a time to enter. However, while the village begins to gain a dark reputation, the elders of the 'core' are becoming bitter- thanks to the passage of time, old stories and tales have been twisted, along with old perceptions on 'shadows' and their connection to light. A hatred for the capital and for the Egyptians kingdom almost as a whole have developed, largely stemming from the fact that in these recent times, the elders have come to believe that the 'three treasures' were stolen as opposed to presented.
Regardless, the power is fading- by Mimir's time, the elders are all that is left of those who can see certain shadows and manipulate them, and even this is faded despite them not realizing it- Mimir and 'Neker', who goes on to become Tragoedia, are the only ones of their generation and the only ones since the elders to develop anything remotely similar.
One could blame it on mixed heritage of course- but the elders are strictly 'core only'. So really, no, it's 'their' fault. Mimir's friend in the 'unbound' shadows in fact, the Red Eyes Black Dragon, hints that it is the village's decline into corruption and detest that caused it in fact, as while it's one thing to defend a people it's another to wrongly accuse and hate another for something that didn't actually happen. All in all history is a mess, so when Mimir starts repeating what the dragon teaches him, things go right to shit.
Now then. As Elna'am has both a 'core' of white-haired citizens and a 'ring' of mixed ancestry, the rest of the country eventually came to see anyone with white hair (and without pale skin, not to say that poor Kisara hasn't had a bit of issues here) as thieves and criminals- ironically, most of the actual thieves from the village are either black/brown haired in origin, or simple dying it to appear as such, but regardless of the fact, in Mimir's time, 'white hair' means 'thief'. (Mimir himself will add in 'dark skin' though, partially because he deals with a heck of a lot more than Egyptians in trade, and partially because be has a weird habit of adding things that don't need to be added. Derp.)
Back to the history of things though... By Mimir's time as an adult, the fading 'core' is more than evident. Out of the relatively large number of people there, only 102 were considered 'white hair'; the extra 'two' are Neker (Tragoedia) and his son, both of whom reside in the palace at this time. The massacre of Kul Elna becomes much more planned out than it seems to have been before though- Aknadin and his men enter in a far more stealthy approach, and after passing through the main 'path' unharmed proceed to force the people to flee to their catacombs- however, rather than allow themselves to become lost, he instead has the men block of all but one of the exits, before entering the final 'main' tunnel. The soldiers are then ordered to round up the people due to the catacombs each being connected (along with the theory of them being connected), while Aknadin and two others he has with him prepare for the ritual.
The soldiers eventually return with 99 white-haired men, women, and children- all others were slaughtered. The 99 are then killed and ritualistically tossed into a pit, over which a mold is placed; gold is poured in, the items are formed, and canon events otherwise occur. (In the manga, we see bodies tossed in the gold.
This would flaw the gold horribly if it was 99 bodies into SEVEN ITEMS.)
As it is, it winds up being Thief King Bakura's blood that completely releases Zorc into the world, and we all know what happened after that...
Tragoedia of course, is the main villain of GX- his son exists for plot related reasons however, and he himself dies rather soon. Not the point though.
In summary- Kul Elna's 'core' beginnings came from freaking ATLANTIS and I am a complete dork.