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The Crystal of Truth is the heart of Thra, contained beneath a mountain. When the urSkeks arrived, they hollowed out the mountain around the Crystal and built a castle of lesser crystals (called the Castle of the Crystal) around the great Crystal. They made the three walls of blocks of crystal, and above the Crystal they made a great portal of three sides. So when the Suns moved over the Crystal, they stood framed in the portal, a triangle surrounding a circle.
After the Second Great Conjunction, when the urSkeks are split into Skeksis and urRu, a Skeksis cracks the Crystal. When cracked, the Crystal changes color from white to violet, becoming the Dark Crystal.
skekTek the Scientist studied the Dark Crystal, and learned how to make beams of light, which he burned into the eyes of Gelfling and Pod People to make them his slaves. He then used the dark light to draw the essence of life, draining it from the living for the Skeksis to drink to slow aging.
The Dark Crystal is healed by Jen, a Gefling, during the Third Great Conjunction. It once again becomes the Crystal of Truth.