One year after the ending of Xenosaga Episode II: Beyond Good and Evil...
The heroine, Shion Uzuki, has come to the realization that the organization she belongs to, Vector Industries, is deeply involved in the cause of the Gnosis phenomenon. With this new knowledge, she decides to resign from her position at Vector and joins an underground anti-U.M.N. organization known as "Scientia" in order to bring Vector's crimes to light. However, after her resignation, a rumor is leaked that the KOS-MOS development project has been suspended. Adding to this mystery is the appearance of an android called "T-elos" who has taken the place of the now suspended KOS-MOS. Various suspicions and intrigues flicker in the shadow of T-elos.
Where will the future of the universe-- the future of mankind-- head towards?
