One year after the events in XenoSaga II: Jenseits von Gut und Böse, Shion has now resigned from Vector Industries after discovering the connection between Vector and the Gnosis outbreak. Working for Scientia, she's now in league with an underground group that seeks to gain information that will expose Vector for what they truly are. During the time, the KOS-MOS project has been canclled in favor of the new found T-Elos Project, head up by Roth Mantel. T-Elos is a battle andorid that is similar to the one known as KOS-MOS. It's now up to Shion and company to gather one last time to figure out the true reason behind Vector, who the Testaments really are and who's the pupper master pulling the strings.