In another world, a mystical crystal is the source of balance and truth, its power ensuring harmony within the universe. However, during a great celestial event, the crystal becomes darkened and cracked, precipitating an age of chaos and division. The splintering of the crystal gives rise to two new races: the malevolent Skeksis, who become tyrannical rulers lusting for immortality, and the wise but feeble Mystics. Now, as the planet faces increasing decay and the dominion of the Skeksis continues unchallenged, a prophecy foretells that a Gelfling, an elf-like creature believed to be extinct by the hand of the Skeksis, will heal the crystal and restore balance.

Upon the death of his Mystic master, a young and naïve Gelfling named Jen is propelled into an epic quest to find the shard that can repair the Dark Crystal. Unaware of the larger forces at play, Jen is told that he must fulfill the prophecy before the Great Conjunction of the planet's three suns. Along his journey, he encounters Kira, another surviving Gelfling, who joins him on the perilous quest. Together, they face a world filled with strange creatures and daunting obstacles. Meanwhile, the Skeksis, aware of the prophecy, set out to stop Jen and ensure their reign remains unthreatened.