Xiao sends the player and Matoi to the planet Harukotan to stop the efforts of Dark Falz [Gemini], who are consuming planets for an unknown reason. [Gemini] reveals that the true purpose of the Dark Falzes is to revive the [Profound Darkness], a failed clone of Xion corrupted by the Photoners that had to be sealed away; the fight between the Photoners and the [Profound Darkness] caused the Photoners to lose their ability to use Photons, prompting them to create ARKS in their place.
After escaping a trap laid by [Gemini], the player and Matoi confront them in the Black Territory's throne room at Harukotan and defeat them, but [Gemini] retaliates by attacking them with highly-concentrated F-Factor in a last ditch effort. The player attempts to sacrifice themselves to save Matoi, but Matoi, unwilling to see the player become the [Profound Darkness], absorbs the F-Factor, becoming the [Profound Darkness]. [Persona] appears and steals the Clarissa that was left behind.
[Persona] confronts the player and offers to join forces to kill Matoi, thereby destroying the [Profound Darkness] and saving the universe. The player agrees to help [Persona], and together they confront Matoi at the heart of Naverius' Corrupted Area. [Persona] sacrifices itself to allow the player to kill Matoi, but Matoi's death causes the player to transform into a new [Persona], creating a time loop.
Using the Divergence Matrix, the player discovers a new fate, and declines the offer to help [Persona]. With the assistance of the Council of Six, the player seals Matoi's power and defeats her in a bid to purify her. Matoi, unwilling to allow the [Profound Darkness] to be fully reborn, attempts to kill herself with a large amount of F-Factor. The player again attempts to sacrifice themselves for Matoi, but [Persona], inspired by the player's ability to defy fate, uses the Clarissa to absorb the F-Factor from both the player and Matoi, causing them to become the [Profound Darkness] in Matoi's place. ARKS successfully repels the [Profound Darkness], but Xiao warns that given the power of its host, it may return.
