Shiva and her cohorts, Varuna and Mithra, begin their assault on ARKS' forces, starting with an attack on Mothership Xiao. During the raid, Shiva successfully takes over the Mothership and gravely wounds Xiao, forcing ARKS to retreat. To save Xiao, the heroes travel to Amduskia, where Sarah merges a fragment of Xiao's consciousness with the body of a dormant Xion clone named Kashina to grant Xiao a new body.

The player and Matoi are sent to Harukotan to thwart a Luminmech invasion and ally with Sukunahime to ensnare Shiva in a trap, but are tricked into fighting Mithra. Mithra is fatally wounded in battle and dies due to the trap, but Shiva regains the upper hand and defeats the heroes. Phaleg, a member of Mother Cluster, intervenes and rescues the heroes.

Phaleg and ARKS are alerted to a Luminmech attack on Earth, and the player returns to the Earth dimension to assist in the counterattack. The player travels across Tokyo, teaming up with allied forces on the planet as well as ARKS member Aika to repel the Photoners. Following the assault, Xiao reveals to the heroes a plan to use Omega to seal Shiva's abilities on a universal scale.