Setting Xenosaga Episode I takes place in a universe based around
science fiction. In the year "20XX", the Zohar—an artifact dating from the beginning of the universe which connects to the realm of a god-like energy dubbed U-DO—was unearthed by an archeological expedition in
Kenya; the Zohar is key to enabling humanity to travel in space beyond the
Solar System. Over 4,000 years in the future, humanity has left
Earth behind to colonize the galaxy following a terrible event. This resulted in Earth's location being lost and the planet being dubbed "Lost Jerusalem"; by the game's events, humanity has adopted a new calendar system dubbed "Transcend Christ" (T.C.), with the game's events taking place in T.C. 4767—equivalent to A.D. 7277. Humanity is now spread across 500,000 planets, with their governments forming the Galaxy Federation. Planets are connected through a time warp travel network called the Unus Mundus Network (U.M.N.). The U.M.N. is managed by Vector Industries, which also controls interests in the Federation's military. Existing alongside humans are Realians, synthetic humans who hold equal status with natural humans. The Federation has come under attack from the ancient alien Gnosis, which begin decimating Federation worlds. As normal weapons are ineffective against them, Vector develops two different weapon systems designed to fight them: humanoid mecha dubbed A.G.W.S. (Anti Gnosis Weapon System), and the similar but more powerful KOS-MOS battle androids. Another hostile faction is the U-TIC Organization, a once-scientific group that now wishes to gain control of the Zohar. A key episode in the game's backstory is the Miltian Conflict, a war between U-TIC and the Federation which triggered the Gnosis' arrival and caused Miltia to be swallowed in a space-time anomaly.
Plot Shion is running final tests on KOS-MOS aboard the
Woglinde when the crew retrieve a Zohar Emulator, one of thirteen replicas of the Zohar. Cherenkov monitors Shion's progress, but is also a U-TIC spy furthering their goal of finding the original Zohar. Following the Zohar Emulator's retrieval, the
Woglinde is attacked by Gnosis. KOS-MOS self-activates and protects Shion's team, in the process killing Virgil with friendly fire to save Shion and Allen. KOS-MOS brings them and Cherenkov on board the
Elsa, which is heading to their destination of Second Miltia. When a Gnosis attacks, chaos' ability to dispel them saves Cherenkov's life. The attack begins mutating Cherenkov, tormenting him with visions of his past as a soldier who failed to adjust to civilian life and killed many people including his wife. During these periods, Shion becomes concerned about KOS-MOS's behavior, and Allen worries about Shion's emotional state. Alongside these events, the cyborg Ziggy is dispatched to rescue the Realian MOMO from U-TIC, as data stored inside her could open the way to the original planet Miltia, lost in a disaster for which her creator Joachim Mizrahi is blamed. Ziggy rescues MOMO and narrowly escapes, fending off attacks by Margulis. Albedo, who is working with U-TIC for his own goals, sets out in pursuit of MOMO. The
Elsa is pulled out of hyperspace and swallowed by a giant Gnosis. During their attempts to escape Cherenkov transforms into a Gnosis. The group are forced to kill the transformed Cherenkov before escaping on the
Elsa and being rescued by Jr.. During the subsequent battle, KOS-MOS activates previously-unseen weaponry and absorbs the attacking Gnosis. While traveling with Jr., the group learn that the Kukai Foundation are gathering and storing the Zohar Emulators created by Mizrahi. Meanwhile, U-TIC uses agents within the Federation to doctor footage of Jr.'s battle with U-TIC and implicate the group in the destruction of the
Woglinde. The group travel to the Kukai Foundation base above Second Miltia, operated by Jr.'s brother Gaignun. They are subsequently held hostage by Federation troops due to U-TIC's influence. With help from an ally of Gaignun, the group retrieve evidence from within KOS-MOS's memory center which can exonerate them. While inside KOS-MOS's memory, the group are guided through a dream-like realm constructed from their repressed bad memories, all the way observed by Nephilim, with whom chaos is acquainted. Shion also meets a vision of Febronia, a Realian woman killed in the Miltian Conflict, who asks Shion to "free" her sisters Cecily and Cathe for the sake of both humans and Realians. Before fulfilling their mission, Nephilim tells them that KOS-MOS was designed to stop the energies of U-DO from entering their reality, an event which caused the original planet Miltia to vanish into a space-time void and could potentially destroy the universe. Due to surviving a Gnosis encounter and remaining human, Shion has the capacity to change the future for the better. During these events, Albedo captures and psychologically tortures MOMO before triggering the "Song of Nephilim", a song which attracts swarms of Gnosis. The Federation fleet try to destroy the Kukai base as it appears to be the source of the Song, but Wilhelm—who has been secretly observing events—arrives with a private fleet that destroys the Gnosis and protects the base. KOS-MOS then uses an advanced weapon to detect the Song's source in a cloaked spaceship. Boarding the spaceship, the group rescue MOMO and fight Albedo, but are stopped by a blue-cloaked man who allows Albedo to escape with a piece of data extracted from MOMO that could grant access to Miltia. Albedo then summons Proto Merkebah, a research ship created by Mizrahi to summon U-DO, and destroys the Federation fleet before aiming Proto Merkebah's weapons at Second Miltia's capital. The blue-cloaked man—revealed to be a resurrected Virgil—observes events before being summoned away. Shion's group infiltrates Proto Markebah and destroys its core while Albedo flees. Escaping Proto Merkebah as it self-destructs, KOS-MOS shields the damaged
Elsa as it enters Second Miltia's atmosphere. ==Development==