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Mothercrystal
There are five mothercrystals, also known as the five "tears", "true crystals", or "shards", that serve to maintain stability in Vana'diel. The five crystals are named Holla, Dem, Mea, Vahzl, and Al'Taieu.
When one dies, their soul is sent to the nearest mothercrystal. The terrestrial avatar Phoenix has the power to manipulate this. However, when Emptiness forms around a crystal, the Empty and Promyvion form from the souls inside of the crystal and their memories.
The Crystal Line was built by the Zilart to open the Gate of the Gods and force their way into Paradise. They encased the mothercrystals in what they named "Arks", modernly called "Crags", and connected them through conduits modernly called "Spines". These connect to Delkfutt's Tower, the control center for the harnessing of their power, which was channeled to Tu'Lia with the goal of opening the gate to Paradise.
But the Kuluu and the Dawn Maidens, with the help of the terrestrial avatars, waged war with the Zilart to stop the attempt. While Bahamut and his wyrm army attacked Al'Taieu, the Kuluu destroyed the Vahzl Crag from a tunnel dug from Pso'Xja. This caused a chain reaction called "The Meltdown", which not only caused a crater that forms the modern-day Sea of Shu'Meyo, but blew pieces of Vana'diel all the way to the moon(Abyssea).
The fifth crystal of Al'Taieu sank to the bottom of Shu'Meyo, but the capital of Al'Taieu's defense system spatially transferred the city to the dimension of Lumoria within the crystal itself. The stone is still part of Vana'diel but still in the capital, meaning the mothercrystal is inside itself forming a paradox.
Rise of the Zilart concerns stopping a second attempt by the Zilart. You succeed, but because the Zilart succeeded in turning the Crystal Line on, Light was drained from the five mothercrystals. Chains of Promathia is the direct aftermath.
The Chains of Promathia Missions introduce the fifth mothercrystal (Al'Taieu), which has lost its light, and the realm beyond it, Lumoria. Technically, Lumoria is in the Al'Taieu mothercrystal, and the crystal is in Lumoria, but it is also in Vana'diel. There is also the region of Limbus, composed of the areas of Temenos and Apollyon. Apollyon was originally called "Lower Promyvion" and is likely a "Promyvion - Al'Taieu" and the "central" Promyvion, whereas Temenos is the Ou'Hpat Obelisk, probably changed after the spatial transfer. Enemies found in Temenos are likely creatures that somehow got inside of the Crystal Line, and it probably connects to the other mothercrystals via the Crystal Line. Enemies found in Apollyon are most likely creatures that have been absorbed by the Emptiness, and it probably connects to the other crystals through the Emptiness found in the Crystal Line.
SPOILER WARNING: Details about the Final Fantasy XI in-game storyline follow.
The five Mothercrystals are fragments of the original Great Crystal which created Vana'diel. The fragmentation of that crystal is what allows Vana'diel to exist. If the five crystals were to reform into the Great Crystal, it would create the Paradise that the Zilart fanatically sought. In this world, only the Zilart and the gods (Altana, Promathia, and the sleeping gods) will be able to exist freely, with the terrestrial avatars reduced to mere beasts. However, as one crystal, Promathia would be reborn and die, thus bring about the apocalypse. Promathia's soul rests inside the fifth mothercrystal. It is possible that the "apocalypse" could also refer to Altana re-shattering the mothercrystal in order to maintain Promathia, thus destroying paradise once again and re-creating the world of Vana'diel anew.
It is interesting to note that the mothercrystals are never referred to by name (Holla/Dem/Mea/Vahzl/Al'Taieu) in-game (except for on the "Light" key items) and instead are called by number ("first three" = Holla/Dem/Mea, "fourth" = Vahzl, "fifth" = Al'Taieu). The five names most adventurers/players are familiar with are likely the terms for the arks built around the mothercrystals and not the mothercrystals themselves.
