A thousand years ago on the planet Thra, a magical crystal cracked, and two new races appeared: the malevolent Skeksis, who use the power of the "Dark Crystal" to continually replenish themselves, and kind wizards called Mystics.
Jen, an elf-like Gelfling taken in by the Mystics after his clan was killed, is told by his Mystic master that he must heal the Crystal, a shard of which is held by the astronomer, Aughra. If he fails to do so before the planet's three suns align, then the Skeksis will rule forever. The Skeksis' emperor and Jen's master die simultaneously. A duel ensues between the Skeksis Chamberlain and General, both of whom desire the throne. The General wins, taking power and exiling the Chamberlain. Learning of Jen's existence, the Skeksis send large crab-like creatures called Garthim to track him.
Jen reaches Aughra and is taken to her home, which contains an enormous orrery she uses to predict the motions of the heavens. She has a box full of shards, from which Jen selects the correct one by playing music on his flute to cause it to resonate. Aughra tells Jen of the upcoming Great Conjunction, the alignment of the three suns, but he learns little of its connection to the shard. Suddenly the Garthim appear and destroy Aughra's home taking her prisoner as Jen flees. Hearing the call of the Crystal, the Mystics leave their valley to travel to the Skeksis' castle. Jen meets Kira, another surviving Gelfling who can communicate with animals, and her pet Fizzgig. They discover that they have a telepathic connection, which Kira calls "dreamfasting," and share memories of being forced from their homes. They stay for a night with the Podlings, who raised Kira after the death of her parents. The Garthim raid the village, capturing most of the Podlings, but Kira, Jen, and Fizzgig flee when the Chamberlain stops the Garthim from attacking them.
Jen and Kira discover a ruined Gelfling city with ancient writing describing a prophecy: the shard Jen carries must be reinserted into the Dark Crystal to restore its integrity. They are interrupted by the Chamberlain, who claims that the Skeksis want to make peace and wants the Gelflings to return to the castle with him, but they distrust him and refuse. Riding on Landstriders, the Gelflings arrive at the Skeksis' castle and intercept the Garthim that attacked Kira's village. While trying to free the captured Podlings, Kira, Jen, and Fizzgig descend to the bottom of the castle's dry moat and use a lower-level entrance to gain access. They are followed by the Chamberlain, who repeats his peace offer; when the Gelflings turn him down again, he buries Jen in a cave-in and takes Kira to the castle. The General reinstates him to his former position, and the Skeksis' Scientist tries to drain Kira's life essence for the General to drink so that he can regain his youth. Aughra, imprisoned in the Scientist's laboratory, tells Kira to call for help from the animals held captive; they break free in response, releasing Kira and causing the Scientist to fall to his death. His Mystic counterpart simultaneously vanishes.
The three suns begin to align as the two Gelflings reach the Crystal's chamber and the Skeksis gather for the ritual that will grant them immortality. Jen leaps onto the Crystal, dropping the shard, but Kira throws it back to him before being stabbed to death by the Skeksis' high priest. Jen inserts the shard into the Crystal, unifying it as the Mystics enter the chamber and the castle's dark walls crumble away to reveal a structure of bright crystal. As Aughra, Jen and Fizzgig watch, the Mystics and Skeksis merge into tall glowing beings, known as urSkeks. One of them explains that they had mistakenly shattered the Crystal long ago, splitting them into two races, and that Jen's actions have fulfilled the prophecy, restoring them and Thra. He revives Kira as a sign of gratitude, and the urSkeks give the Crystal to the two Gelflings so they can "make [their] world in its light." They depart, leaving the crystal castle standing in a now-rejuvenated land.
Who does Kira have a telepathic connection with?
Jen