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.