The Dark Crystals (闇のクリスタル, Yami no Kurisutaru?) are the counterparts of the elemental Light Crystals, and are referred to as "Dark" for being either hidden from the rest of the world or aligned to darkness itself.
A Black Crystal ("Dark Orb" in the NES version) can be found in the middle of the Chaos Shrine. While the game's plot never explicitly states any detail, Garland used this Crystal as a means of connection to the 2000-year-old past, possibly to communicate with the Fiends of that time, and possibly to travel there upon death. After the Warriors of Light restore light to the four elemental crystals, the Black Crystal disappears in a flash, and the pedestal where it once stood allows travel 2000 years into the past.
The Dark Crystals of Fire, Wind, Earth, and Water of the World of Darkness are the counterparts to the original Crystals from the world of the Warriors of Light. As the Warriors of Light are the envoys of the Crystals of Light, the Crystals of Darkness also have their own four Warriors of Darkness.
When the Warriors of Light enter the World of Darkness to defeat the Cloud of Darkness, they discover the Crystals of Darkness, which are also kept by monsters, who strengthen the Cloud of Darkness. Ahriman guards the Dark Earth Crystal, Cerberus guards the Dark Wind Crystal, Echidna guards the Dark Water Crystal, and the Two Headed Dragon guards the Dark Fire Crystal.
Four Dark Crystals exist in the Underworld, to counter the four Crystals of the Blue Planet's Overworld. However, the location of only two Crystals is known: one is kept by the dwarves at the Dwarven Castle, while another is kept in the Sealed Cave. Golbez steals the Dark Crystal from the Dwarven Castle, but the seal on the cave protects the last Dark Crystal from him.
Eventually, Giott fears that Golbez will be able to break the seal by force, and gives the party Luca's necklace to open the seal. The party retrieves the Dark Crystal, but as they leave, Golbez asserts his mental domination of Kain and seizes it from the party.
The Dark Crystal is silently shedding its light inside the Crystal Chamber in the Sealed Cave. The entrance to the Crystal Chamber is guarded by the Demon Wall. After Cecil and company arrives inside the chamber, they find Rydia lying on the floor of the chamber.
The four Dark Crystals, along with numerous other crystals of both light and darkness from other worlds, appear. Rydia and Luca arrive too late at the Dwarven Castle to prevent the Mysterious Girl from taking the Dark Crystal there. The two again retrieve the Dark Crystal from the Sealed Cave, but the Mysterious Girl arrives and takes it from them. The Dark Crystals, along with the Crystals of the Overworld, are retrieved from the Depths of the True Moon.
The large crystalline rocks scattered around the Giza Plains are known as Dark Crystals. During the Dry they absorb sunlight, which can be drained into Shadestones to create items known as Sunstones.
A dark crystal resides on top of the Flying Tower, which adventurers constantly try to destroy. Inside the Crystal resides Darklord Craydall, who fills the tower with the power to sustain the monsters inside it once the Miasma cleared. It is also said that his daughter Mira draws her powers from the crystal.
The Dark Crystals are a crucial part of the Emperor's scheme, having manipulated Jecht to fight Tidus so that he would receive the crystal Cosmos implanted in him during the last cycle of conflict while he was a warrior of Cosmos. As a result, because Jecht was infused with the powers of Chaos, the Crystal he received was attuned to darkness and the Emperor seized the crystals created from Jecht with the intent that, as the Warriors of Cosmos survived the death of their goddess, the Emperor would likewise survive Chaos', and would be free to rule all existence unopposed with both gods dead. The Dark Crystals the Emperor speaks of are never seen in-game.
One of the Components that can be created through Battlegen is the Blackcrystal Sliver, found in the Chaos Shrine as a reference to the Dark Orb from the first game.