第1話: T.C. 4767、Gnosisの攻撃によりKOS-MOSが起動する直前、Shion UzukiはZohar Emulatorと遭遇する。

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In the year T.C. 4767, an astronaut touches a mysterious golden rectangle (a Zohar Emulator) and disappears. The episode shifts to Shion Uzuki, a Vector Industries scientist, testing an anti-Gnosis battle android called KOS-MOS. Vector's KOS-MOS team is deployed on the Woglinde spaceship in case of a Gnosis attack. While delivering her latest report, Shion sees the Zohar Emulator in the hangar and almost touches it after seeing a mysterious girl inside it. After Shion delivers her report, after deciding she can't sleep, she heads to the Realian maintenance room to see what's new. There, Shion meets a 100-Series Realian, who she talks about free will with. Luis Virgil enters, calling the Realian girl a freak, and Shion defends the Realian. The Gnosis attack the Woglinde. The episode ends as KOS-MOS is self-activated. (Source: Xenosaga Wiki)