When the Warrior of Light arrives in the wood with Thancred, Minfilia, Urianger, and Emet-Selch, she initially doubts the Warrior of Light's identity because of how much light they have absorbed. Upon learning that their mission is to find and slay the Lightwarden hiding in the forest, she helps them travel deeper into the woods to reach Yx'Maja, where the ruins of the Ronkan Empire are found.

Together they discover where the Lightwarden is hiding and enter the ruins to unlock the path, but are attacked by Ran'jit and an emissary of Eulmore, who tell them they have poisoned the Night's Blessed. During the ensuing fight Ran'jit and the emissary are lost down a pit, and Y'shtola dives in after them, seemingly sacrificing herself to get the antidote from them to her friends. They realize that she used the Flow spell again to escape, and Emet-Selch pulls her out of the Lifestream as a gesture of good faith. After destroying the Lightwarden, Y'shtola examines the ancient paintings in the cave and wonders as to their significance. Emet-Selch explains that they tell the story of how his people long ago summoned Zodiark and Hydaelyn, and after the latter defeated the former, Zodiark was imprisoned and the world divided into fourteen parts: the Source and its thirteen reflections.

After helping to defeat the remaining Lightwardens, Y'shtola follows the Warrior of Light into the Tempest to confront Emet-Selch. Comparing the underwater ruins to the painting in the Ronkan cave, she concludes that they are the remnants of the ancient Ascian city of Amaurot of which Emet-Selch spoke. After Emet-Selch's defeat, she returns to the Night's Blessed while the Crystal Exarch looks for a way to return their souls to the Source.