Naia has been rescued by Gurjin and makes a plan to save Tavra, Kylan, Onica and Amri from SkekSa. The twins make their way into the chamber where their friends are being held and successfully distract SkekSa and help the others escape. As the others escape, Amri is separated and Naia goes to find him, but once she does they are ambushed by SkekZok the Ritual Master. As Gurjin and SkekSa join them, a fight ensues in which SkekZok mortally wounds Naia. Gurjin uses magic similar to her own to heal her, which confirms the validity of SkekTek the Scientist's theory. Before the Skeksis can seize the Gelfling, Naia dreamfasts with Vassa, SkekSa's tortle. The beast floods its insides, incapacitating the Skeksis and allowing the Gelfling to escape, after which Naia loses consciousness.
Naia wakes twelve days later in the Valley of the urRu, where she discovers that UrSan the Swimmer found her and her friends and transported them down the Black River in her boat. Her friends introduce her to UrZah the Ritual Guardian and UrTih the Alchemist. They are reunited with UrLii the Storyteller, who informs them that reinforcements were sent to the Grottan Sanctuary and freed SkekLi the Satitist. UrSan informs them that UrVa the Archer is badly wounded and is being treated by UrSu the Master. They visit him and Naia asks how they can defeat the Skeksis without killing the UrRu, to which UrVa assures her that there is a way. UrSu then shows them a vision in which he reveals that the UrSkeks came to Thra during the first Great Conjunction and were split into the UrRu and the Skeksis during the second, which became known as the Great Division.
Naia and Amri explore the valley and discover that while it is still mostly pure, the Darkening is slowly gaining a presence there, which they are unable to heal. The Gelfling then prepare to leave, with Naia, Gurjin, Kylan and Amri going to Sami Thicket and the Swamp of Sog and Tavra and Onica going to the Caves of Grot and Stone-in-the-Wood. Before they leave, they bid farewell to UrSol the Chanter and make him promise to tell the other UrRu how thankful they are for their hospitality.
Naia, Gurjin, Kylan and Amri reach Sami Thicket and meet with Maudra Mera. She refuses to light the fires of resistance, as she fears the Skeksis and Maudra Fara and the Stonewood Clan recently attacked the Castle of the Crystal and were defeated and captured. She informs them that the Drenchen Clan are planning to attack Sami Thicket and that they must be ready for them. Upon seeing guards from the Castle, Naia and Amri set the camp on fire and scare away the Landstriders, angering Maudra Mera, as well as Gurjin and Kylan, with their recklessness.
Maudra Laesid and her soldiers enter Sami Thicket to meet with them and discuss terms. Kylan tells a song of what can be if the clans unite, which inspires the Spriton Clan to light the fires of resistance and rise againts the Skeksis with the Drenchen. Through the flames, they discover that Rian has inspired the Grottan Clan to light the fires of resistance.
The group travel to the Swamp of Sog with the Drenchen and discover that there is unrest among them, including Naia's own family. The Smerth-Staba is infected by the Darkening and Maudra Laesid wishes to abandon it while Bellanji wishes to save it. The swamp is soon attacked by SkekSa, who demands that Naia and Gurjin be handed over to her. The Drenchen refuses and SkekSa causes further damage to the tree by throwing thunder eggs at it. UrSan arrives and attacks her counterpart, with Laesid considering that they should kill SkekSa even though it will lead to UrSan's death. At Naia's urging, she decides to seek another way. Under Naia's leadership, the Drenchen chant the song of Thra to the tree, allowing Laesid to use its magic to trap SkekSa in an apeknot tree. However, this comes at the cost of her own life. Devastated by her mother's death, Naia must rise up as the new Maudra of the Drenchen Clan.
As the Drenchen ride to Stone-in-the-Wood on Landstriders, Amri admits to Naia that he has feelings for her and requests that he accompany her wherever she plans to go should they manage to defeat the Skeksis. As they near the village, they meet Maudras Mera and Fara, who has escaped from the Castle with her troops. In the village, they find Rian, who is accompanied by Deet of the Grottan Clan and has recovered the Dual Glaive from the Tomb of Relics. He then lights the fires of resistance and urges the other clans to join them and rise up againts the Skeksis. SkekSo the Emperor interrupts the message and warns that he and his fellow Skeksis will descend on Stone-in-the-Wood and kill any Gelfling who defy them.
The Gelfling make preparations for the upcoming battle and at dawn the Skeksis reach the village. Rian stands alone in the centre as they advance on him and the others remain hidden, attacking the Skeksis with Deet's smoke bombs and disorientating them. On SkekSo's orders, SkekMal the Hunter attacks Rian and forces him up to the village's plinth. Naia attempts to help him, SkekSo blocks her path and attacks. She gains the upper hand on him, but SkekSil the Chamberlain grabs her and holds her still while the Emperor prepares to deliver the killing blow. Fara attacks SkekSo and allows Naia to escape, but is killed in the process.
As the other clans arrive and attack the Skeksis, Naia goes to aid Rian. Periss gives her a lift on his Crystal Skimmer, though once they reach the plinth SkekMal shatters the Dual Glaive. He prepares to kill them, but UrVa communcates with them through his counterpart before driving an arrow into his own heart, killing SkekMal in the process. In the shattered remains of the Duel Glaive, Rian finds the Shard of the Division. It strikes fear into the Skeksis, who prepare to attack. Rian encourages the Gelfling to drop their weapons and join hands, the magic of which creates the Wall of Destiny and causes the Skeksis to flee the village in fear.
As the Gelfling examine the carvings, Aughra arrives and congratulates them on their victory and for finding the way to defeat the Skeksis. The Gelfling then mourn those who died in the battle and Naia meets with Maudras Mera, Ethri, Seethi, Argot and Seladon, who all agree to allow Gelfling of any clan to live in their regions, cementing unity and solidarity within the race.
Rian and Gurjin set out for the Castle to find a way to return the shard to the Crystal while Kylan, Tavra and Onica choose to stay in Stone-in-the-Wood and interpret the markings. Naia and Amri set out for the Swamo of Sog, knowing that although the future is uncertain, the Gelfling are more united than they have ever been.