 It is one year after the events of Xenosaga Episode II. Shion Uzuki has resigned from Vector Industries after discovering that they are partially responsible for the Gnosis outbreak which have plagued mankind. Shion now works for Scientia, a secret organization dedicated to resisting Vector. The KOS-MOS project has been abandoned, seemingly replaced by the mysterious T-Elos project. Shion and her compatriots must embark on their final adventure to determine the fate of the entire universe...