The player and Xion are approached by Luther, the founder of ARKS and the last remaining Photoner, who desires to gain omniscience by absorbing Xion. Following a preliminary expedition to the planet Wopal, the player meets Xiao, a version of Xion from an alternate universe. Xiao bestows the power of time travel to the player and sends them back in time to rescue Zeno and ARKS operative Ulku to thwart Luther's plans.

Xion reveals that she is the Mothership's core and sends the player and Matoi to rescue her from Luther. During the expedition, Matoi is revealed to be the true wielder of the Clarissa. Luther successfully absorbs Xion and gains omniscience, but is defeated by the heroes. Luther's anger over his defeat causes him to transform into Dark Falz [Luther] and take over the Mothership, but Xiao intervenes and summons his own Mothership, saving ARKS from imminent peril. Xion helps the heroes escape from [Luther], but perishes.

Xiao sends the player ten years into the past to meet Klariskrays II, a member of the Council of Six and Matoi's former identity. Seeking to provoke Klariskrays II to further his schemes, Luther helps an older version of Dark Falz [Apprentice] attack an ARKS Ship. During the attack, Klariskrays II confronts [Apprentice], but is deterred by [Apprentice]'s powers. [Persona] comes to Klariskrays II's aid but impales her shortly after, causing Klariskrays II to transform into a Dark Falz. The player intervenes and repels [Persona], who is revealed to be the player from an alternate timeline. The Clarissa partially purifies Klariskrays II, but Klariskrays II loses her memories and is sent ten years into the future as a result.