After finding herself transported to Miltia 15 years in the past, Shion finds the rest of the group and investigates the area to find out what happened. Along their way, they come across Virgil engaged in combat with U-TIC realians. Seeing that he is badly injured, they decide to help him despite knowing he is the Blue Testament. They soon find an old church where they meet Febronia with a young Shion and Kevin. Febronia offers to be an organ donor to save Virgil’s life, and an emergency operation is conducted to rescue him. After the operation proves to be a success, Virgil, who has a deep prejudice towards Realians, gets to know Febronia and begins to reevaluate his views. Meanwhile, the group reconvenes with the crew of the Elsa to discuss their current predicament. The professor reveals that unless they can find a sufficient power source, it will be impossible to return to their own time. Allen also reveals to Shion that KOS-MOS’s black box has been damaged beyond repair, and without the help of Kevin, her original creator, she will never reawaken. Shion, despite warnings from Allen and the others about meddling with the past, decides to go into the city and discovers key truths about Joachim Mizrahi and the Zohar project that led to the disaster on Miltia. Most importantly, she learns that her father, Margulis, and Mizrahi were attempting to control the Zohar through experiments performed on both her mother and herself. She also learns that Kevin was a key member of Mizrahi’s team and finds baseline designs and code for KOS-MOS that allow the Elsa’s crew to repair her. As Allen and the professor work on reviving her, the ship is attacked by Voyager, who is beaten back by a redesigned KOS-MOS. With KOS-MOS repaired, the group then focusses on finding a sufficient power source to return to their own time and settle on conducting an operation to steal the vessels of Anima stored in the U-TIC secret base of Labyrinthos. While conducting the mission, Shion learns that U-TIC, under Kevin’s supervision, had developed the combat Realians that slaughtered all the people of the city and killed her mother during the Miltian Conflict. As the group attempts to escape with the vessels of Anima, Shion realizes that her mother is being transferred to the treatment facility where she will eventually be killed and decides to go after her rather than escape. Though the group wants to help her, they are overwhelmed by U-TIC forces and have no choice but to retreat. Shion is then confronted by the Red Testament, who reveals his true identity as Kevin Winecott. Shocked by this revelation, Shion freezes up and is captured by U-TIC.