Thousands of years into the future, man exists only in deep space. Brutally opposed by a merciless alien race, humanity faces an uncertain destiny as it unlocks the secrets of the Universe in search of the ultimate truth.
The story of Xenosaga III starts a year after "Xenosaga II" ended. Shion has resigned from Vector Industries after learning that the company is deeply connected to the appearance of the Gnosis. She instead joins Scientia, an underground organization working to unveil Vector's secrets in order to bring them down.
Four-thousand years into a war-torn future. Earth has been abandoned and mankind forges its existence in deep space, locked in eternal confrontation with the malevolent, alien Gnosis. With sophisticated weapons and robotics technology, humankind wages an epic battle for survival. In a desperate bid to fend off extinction, the search continues for the Zohar, a legendary artifact rumored to be capable of eradicating the Gnosis and ushering in an era of universal peace.