Six months since the destruction of the Old Miltian Star System with the appearance of Abel's Ark, Shion Uzuki uncovers information that leads into Vector being responsible for the following crisis known as Gnosis Terrorism. She resigns Vector, and joins Underground anti-UMN organization, Scientia. An organization dedicated towards exposing Vector's crimes. Another Six Months pass, and Shion receives an invitation from her ex co-worker Allen Ridgeley into Fifth Jerusalem, only to find that the Kos-Mos project is to be replaced by the T-Weapon project. The project's primary units are the remake of the Omega Weapon which was cause of the destruction of Miltia, and a Female Battle Android resembling Kos-Mos, known by the name of T-elos. Following the appearance of a chunk of land in outer space, Shion and her group find themselves involved into twists and desperate measures to accomplish a prophecy, as the galaxy's major factions go into conflict leading into what could be the end of the universe.
—Aldo Della Rocca