Brother against brother, as the universe cries out
Together with the restored Elsa, Shion and her friends break through the Immigration Fleet's forces and land on Old Miltia. They enter the Labyrinthos, to seek the Original Zohar. At the end of it all, they find the Patriarch has already activated the Original Zohar to power a secret weapon - the Proto-Omega. They attempt to free Febronia's sisters, but the machine cannot be stopped, as it draws power from U-DO as well. When all hope is lost, four cloaked figures appear, calling themselves the Testaments. They remove the Patriarch and Proto-Omega, but before they can claim the Zohar, Albedo appears to claim the power for himself... as the Elsa flees the planet.
As a Space-Time Anomaly forms around the ruined planet, Jr. returns alone, to confront his other half for the last time. Facing all his inner demons and conflicts, Jr. eventually overcomes Albedo and brings him to eternal rest. As the Anomaly collapses, a huge Gnosis ship larger than a planet warps in and retrieves it, before disappearing once more.
On the Dammerung, the CEO of Vector, Wilhelm, watches the events with interest. He knows the Gnosis Ship as "Abel's Ark" and chaos as "Yeshua." As the various characters celebrate a job well done, Wilhelm meets with the Testaments who serve under him and introduces them to their newest member - Albedo, the White Testament. Wilhelm welcomes him as a weaver of the eternal circle of Zarathustra as the game draws to a close.