Jen, a Gelfling, was orphaned as a child when his mother, father and his entire village were destroyed by the Garthim in the great Gelfling genocide. Jen himself would've been killed, too, had the Mystic urSu not happened upon him. As Jen later recalled, urSu was "big, and made the bad things go away," rescuing Jen. The infant was taken in by the Mystics and raised and educated by them and he came to regard them as his adopted family...the only one he knew in fact.
Some time in Jen's adolescence, urSu fell gravely ill and summoned Jen to his bedside, telling him that he and he alone could save their world from dying. He was told only that he must seek Aughra, the Keeper of Secrets, on her hill and obtain a shard of the Dark Crystal, before urSu died, to Jen's sadness. Urged on bu urZah, Jen undertook his quest to Aughra's hill.
There, in her observatory, he had to pass a test to deduce which of three shards was the correct one. He figured out which one it was by playing his flute; the clear shard resonated from the music and briefly glowed purple. Before Aughra could tell Jen what to do with the shard, a troupe of Garthim attacked. Only Jen escaped, and he fled, assuming Aughra had been killed. The following morning he made the startling discovery that he was not in fact the only Gelfling left alive: a female named Kira, along with her pet monster Fizzgig, saved him in the swamp.
The three returned to the Podling village where Kira lived, where Jen told Kira what he knew of the shard and the "Great something-or-other." Garthim raided the village, and Jen escaped with Kira and Fizzgig. Jen blamed himself for the attack on the village, but Kira sadly reassured him he wasn't to blame; "The Garthim have always come."
They spent the night in the woods. In the morning, they discovered the ruins of a Gelfling city. Here, Jen's ability to read allowed him to interpret a wall mural explaining that a Gelfling must heal the Dark Crystal before the next Great Conjunction, so that "what was sundered and undone, shall be whole, the two made one." On Landstriders, the two Gelflings rode to the Castle of the Crystal and infiltrated it via the sewers, where they were captured by the Skeksis Chamberlain.
Jen stabbed the Chamberlain with the shard. Enraged, the Skeksis buried him in a cave-in, and then made off with Kira. Jen survive and dug his way out. Accompanied by Fizzgig, he explored the castle and was attacked by Garthim. To escape them, he crawled through a hole in the wall and found himself in the castle's fiery main shaft. Climbing up he accessed the destroyed Chamber of Life where he was reunited with Aughra. She hastily told him Kira had been and gone, and that soon the Great Conjunction would happen.
Jen proceeded immediately to the Crystal Chamber where he found the object of his quest floating above the very shaft he had climbed earlier. The Skeksis entered and gathered around it, preparing for the Conjunction, when the Chamberlain noticed the Gelflings. Attacked by more Garthim, Jen leaped onto the Crystal, but dropped the shard. At the cost of her own life, Kira retrieved the shard and threw it to Jen even as the Skeksis High Priest stabbed her.
Enraged and mournful, Jen thrust the shard back into the place just as the combined light from Thra's three suns shone through the skylight. An explosion of energy flung him off of the Crystal and to the floor. He cradled Kira's dead body as the Skeksis panicked, and then the Mystics entered, and he beheld the two made one, as the two groups merged into the UrSkeks.
The leader, UngIm, addressed Jen and explained how they had tampered with the "pure Crystal." Restoring Kira to life, the UrSkeks left the Crystal in the Gelflings' care. Jen and Kira would make their world in its light.