Shion was attacked by the Gnosis that had infiltrated the ship. As she lost consciousness she saw an image of a mysterious girl that called herself Nephilim. Shion was helpless and knew she would die, but KOS-MOS self activated and saved her. Rendezvousing with Allen and Virgil after being saved by KOS-MOS, Shion attempted to escape from the Woglinde. KOS-MOS defeated the numerous Gnosis that attacked them, but during the battle KOS-MOS shot and killed Captain Virgil along with the Gnosis in order to save Shion. KOS-MOS felt no remorse for killing Virgil and told Shion, who was appalled at her actions, that she is a weapon. Shion was unable to accept what KOS-MOS declared and escaped from the Woglinde with Allen in the escape pod. After her escape from the Woglinde, Shion Uzuki was rescued by a space cargo vessel, the Elsa, and met a boy named chaos, who possessed strange powers. In front of Shion, chaos disintegrated a Gnosis just by touching it. She was surprised by his power while chaos silently smiled at her. The captain of the ship, Matthews, accepted KOS-MOS's high-handed request and headed for Second Miltia with Shion and Allen. Meanwhile, the cyborg Ziggy was on a lone mission on the asteroid Pleroma by the request of the Galaxy Federation's Contact Subcommittee to retrieve the kidnapped 100-Series Prototype Realian MOMO from the U-TIC Organization. MOMO was targeted by the U-TIC commander Margulis due to the secret document known as the Y-data that was imbedded into her subconscious domain by Joachim Mizrahi. Ziggy was able to safely rescue her and escape Pleroma with a small vessel, but was pursued. While on their way to Second Miltia, the Elsa detected Ziggy and MOMO, who were under attack. They destroyed the U-TIC Organization's Auto-Tech and saved them. After conferring with Juli Mizrahi, Ziggy and MOMO stayed on board the Elsa to go to Second Miltia. Later, the Elsa rendezvoused with the heavily armed ship, the Durandal, that was investigating the U-TIC Organization. Shion and the others met a boy named Jr., who was a member of the board of directors of the special foundation known as the Kukai Foundation. Jr., with ties to the Second Miltia government, understood the situation surrounding MOMO and invited them to stay at the Kukai Foundation. They get a little respite at the colony owned by the Kukai Foundation courtesy of the representative director, Gaignun Kukai. Margulis, who had been watching them, created a trap for the Foundation in order to obtain the Y-data that lay dormant in MOMO. By Margulis's scheme, the Foundation was surrounded by a Federation fleet on grounds of treason against the Federation. They were arrested and detained by the army, but they proved their innocence witht he battle data recorded in KOS-MOS. (Continued in Der Wille zur Macht)