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. The fifth crystal of Al'Taieu sunk to the bottom of the Shu'Meyo seafloor during the battle between the wyrms and the Zilart, but the capital of Al'Taieu's defense system spatially transfered the city to the dimension of Lumoria, yet the stone is still part of Vana'diel but still in the capital, forming a paradox.

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 Rise of the Zilart Missions concern themselves with the first four mothercrystals and the arks (or crags) built around them. The Crags of Holla, Dem, and Mea, as well as the destroyed Crag of Vahzl were built by the Zilart to harness the power of those mothercrystals. Delkfutt's Tower was the control center for the harnessing of this power, which was used to power Tu'Lia, with the goal of opening a gate to Paradise. The Crystal Line was the conduit used to carry the power from the arks, known also as crags.

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 it and it 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.

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.

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