Tensions mount as the survivors struggle to rebuild their lives among the ruins of Japan. As arguments become heated, Haruka questions her sanity as she begins to see Ayato in various places. Meanwhile, Quon prepares to make her final move.

The RahXephon has transformed into its final state and the battle between the Xephons has begun. The outcome will not only determine the fate of Ayato and his loved ones but also the world.