At GHQ Headquarters, Gai makes a worldwide announcement that the Leukocyte will destroy the world on December 25th. The remnants of Funeral Parlor, the Kuhouin Group and Tennouzu High School students escape Japan on a ship, where Shibungi, released by Gai, gives Shu a journal written by Kurosu detailing the history the Apocalypse Virus. In 2013, Keido, a college professor researching on Genomic Resonance, befriended his student Kurosu, who was interested in his research. In 2017, Kurosu married his colleague named Saeko Shijou, moving in with her after she became pregnant with Mana. In 2022, a meteorite crashed on Earth, first discovered by Mana and Saeko. In 2023, Keido and Kurosu discovered a virus inside the meteorite, which reacted when the Genomic Resonance was used, meaning Mana and Saeko were infected. Yu, the representative of Da'ath, offered to help them with their research, believing that the virus will start the Apocalypse. Yu ordered Kurosu to disallow Saeko to have an abortion during her pregnancy with Shu, since Mana chose Shu as her mate to start a new race after the Apocalypse, but after Saeko died by the virus after childbirth, a grieving Kurosu refused to work with Da'ath anymore. Keido later joined Da'ath by helping them find a more suitable mate for Mana by experimenting on children with the Apocalypse Virus. In 2028, Kurosu, who have since kept busy on finding a cure for the virus, fell in love with his new assistant Haruka, who also took care of Kurosu and his children, eventually marrying him. At the same time, Keido adopted Gai, who was a victim of child trafficking, but subjected him in the experiments, eventually leading Gai to run away and encounter Shu and Mana on the beach. In 2029, on the day of the Lost Christmas incident, Keido became bitter and jealous after learning that Kurosu managed to find a cure for the virus by creating the Void Genome, but wanted to keep the burden creating it on himself. When Kurosu caught Keido in his office, Keido killed Kurosu and stole his research before Haruka found her husband's body. In the present, Haruka reveals that Mana was able to enter Inori's body during the second outbreak and slowly taking control of her because the Voids that Shu have been extracting are pieces of Mana herself. When Shu tries to return the Voids back to his friends, they all refuse already knowing that he is risking their lives, and Shu forgives Souta for betraying him. Shu, Tsugumi, Ayase, Argo, Shibungi, Haruka and Kurachi set off with allies from the United Nations to attack GHQ Headquarters.

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