Asuna Yuuki's involvement in the Alicization arc starts with her investigation into Kazuto Kirigaya's poisoning. This leads her to infiltrate the Ocean Turtle facility disguised as Rinko Koujiro's assistant, where she uncovers Project Alicization's objective: developing artificial fluctlights for military use and its connection to the Underworld simulation. During an external attack on Ocean Turtle aimed at capturing Alice Zuberg, Asuna remains in the real world, coordinating defenses while monitoring Kazuto's comatose state.

She later accesses the Underworld using the "Stacia" super account, granting system-level authority to manipulate terrain and geology. Her Stacia avatar manifests with chestnut hair, light brown eyes, pearly-white armor, and a layered skirt. Arriving at the war's climax, she immediately creates massive fissures to divide enemy forces, strategically wielding her administrative powers to aid allies.

Within the Underworld, Asuna assumes battlefield command alongside Integrity Knight Alice Zuberg, temporarily resolving initial tensions through combat. She facilitates the integration of real-world players (including past allies) with Underworld natives by explaining the simulation's nature and their shared goal to protect it, coordinating diverse factions against the invading Dark Territory armies.

A significant moment occurs when she locates the catatonic Kazuto; his fluctlight responds to her voice, triggering his gradual recovery despite severe damage. Her actions consistently prioritize protecting others, manipulating terrain to shield allies and employing diplomacy to maintain coalition unity. Following the war, she participates in stabilizing Underworld and securing Alice Zuberg's transition to the real world.