Jen and Kira discover a ruined Gelfling civilization with ancient writing describing the prophecy: "When single shines the triple sun, what was sundered and undone shall be whole, the two made one by Gelfling hand or else by none." skekSil interrupts them and tries to deceive the Gelflings into believing that theonly reason for the genocide was prophecy so that they will follow him back to castle.
The Gelflings, however, flee and arrive at the castle on Landstriders, where they intercept Garthims that had previously pillaged Kira's village. Kira, Jen, and Fizzgig drop into the Castle's dry moat (revealing Kira has wings) and make their way through the catacombs in order to free the Podlings.
But they are quickly intercepted by SkekSil, who attempts to take them to the other Skeksis when they refuse him further. In defiance, Jen stabs skekSil's hand with the Shard (which in turn causes his Mystic counterpart urSol to receive a similar wound), and SkekSil, enraged, buries Jen alive and takes Kira.
After being reinstated, SkekSil regained his position as Chamberlain and gave Kira to the Scientist. There, she was drained of her life essence so that the Skeksis could drink it and regain their youth. The Scientist, imprisoned in Aughra's laboratory, tells Kira to summon the captive animals for assistance; they break free in response, freeing Kira while also causing skekTek to plummet down a crystal shaft to his demise. His Mystic counterpart, urTih, vanishes in a burst of flame the instant Kira leaves and before Jen arrives. Simultaneously, Aughra frees herself.
The three suns begin to align as the Gelflings rejoin at the Crystal Chamber, and the Skeksis gather for the magic that will make them live forever. When the Garthim are sighted, Jen flies to the Crystal and drops the Shard. Kira picks it up after Fizzgig is thrown down the shaft by skekUng, but Aughra rescues him shortly thereafter.
Kira throws the Shard back to Jen and is fatally stabbed by the Ritual-Master, skekZok. The brokenhearted Jen fulfilling the prophecy by plunging the Shard into the Dark Crystal. When the Garthim disintegrate, the Podling slaves regain their power while the dark energy surrounding the Castle disappears to reveal a pure structure.
The urRu appear and utilize the Crystal to meld themselves with the Skeksis, transforming them into something more like their former selves: angelic urSkeks. The urSkeks' leader tells Jen they broke the Crystal a long time ago, which caused them to become two different races and ruined Thra. He says that because of Jen's courage and Kira's selflessness, they're fixed now. After the urSkeks revive Kira, they are grateful and ascend to a new level of existence. They leave behind the Crystal of Truth for Jen and Kira on the now-thriving Thra.