 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.