Shu arrives at the Undertakers Headquarters at Roppongi Fort where Gai introduces him to the Undertakers and plans to hold a trial for Shu before he can officially join them. Gai assigns Ayase as Shu's instructor while he leads a mission to take over "Leukocyte". Ayase dislikes Shu but is only training him because it was Gai's orders and Shu has to pass the trial as Ayase has his pen, unaware it's a transmitter but she will only give it back after passing the trial. After some hard training, Shu encounters Inori, telling her that he joined the Undertakers because of her and asks her if she will join him if he wanted to leave the Undertakers. But Inori tells him she won't because Gai gave her a life and purpose and claims Gai told her to use his feelings for her to join Undertakers before entering Gai's room. Dejected, Shu runs away and bumps into Ayase, who consoles Shu and gives him some encouragement for tomorrow's trial. Unknown to both of them, despite what it seems, Inori is actually giving Gai a blood transfusion. On the day of trial, Shu has a mock battle with Ayase's Steiner where if he gets past Steiner and into the vehicle behind it, he will pass the trial. Shu succeeds the task after using Arugo's Void to blind Steiner and get into the vehicle where Ayase and the Undertakers congratulate Shu of the becoming one of them. Just as Kenji arrives, the Undertakers receives a troubling report from Tsugumi. Gai earlier led a team to intercept the arrival of mercenaries and Endlaves at an airport but their position was shoot by Leukocyte, an orbital satellite laser.

Since his failure to save Jun, Shu is suffering traumatic memories of the Apocalypse Virus and hallucinating seeing people being infected which cost the Undertakers a mission to stop a convoy. Unwilling to join them anymore, Gai kicks Shu out the Undertakers. Retuning home, Shu finds Inori leaving but not before giving him her new song but he slaps it after getting another panic attack. Depressed, at school Shu ask Hare if he can be close to her but she slaps him as she isn't his replacement for Inori and he isn't the Shu that she loves and knows. Meanwhile, Major General Yan has put Shuichiro under house arrest for stealing the Apocalypse Virus meteorite and plans to have it transported overseas which Gai and Undertakers plan to attack the plane transporting the cargo and retrieve it. However, unknown to both the GHQ and the Undertakers, Seiga and the Anti Bodies have other plans and start vaccinating themselves. As Gai and his team get inside the transport plane, they find it empty and realize too late it is a trap. Seiga activates a genetic resonance broadcast at Tokyo Tower which causes the meteorite to spread the virus all over Tokyo and causing chaos. With both the GHQ and the Undertakers in disarray due to the virus, the Anti Bodies attack both of them and rescue Shuichiro from his confinement which Shuichiro watches the chaos from GHQ Headquarters and declares he will finish what he started 10 years ago.

Argo is airdropped into Loop 7 as part of his mission to rescue Arisa as the head of Shanghai's Ming Hua Group, who is in love with her and in exchange for rescuing her, promises her grandfather that he will have the Association of Asian Nations intervene in Japan. As he explores the area, he witnesses Tennouzu students with Void weapons attacking another group of survivors for vaccines and has one of them follow them to Tennouzu to see her Void. Recognizing Argo as a member of the Undertakers, they take him to meet Shu, where he is shock to see how much Shu has change. Since Hare's death and implementing the ranking system, Shu has ruled the school with an iron fist by making students with Void weapons as his Secret Service who enforce his rule and maintain order while searching for other potential void users in the area to join Tennouzu while the F-ranked void users remain infected with the virus and are ordered to work repairing a battleship they will use to escape Tokyo in exchange of getting vaccines.

Ayase, Tsugumi and Argo are shocked on what Gai has done and Daryl is bewildered upon given orders to protect Gai, their former enemy. An UN Stealth Bomber attempts to bomb them but Gai sacrifices the student ring leaders of the coup to destroy the plane. After destroying their Voids, Gai orders Ayase, Tsugumi and Argo to join him or die but are rescued by Daryl who is protective with Tsugumi and blames Gai for making him kill his father. In the confusion of Daryl's insubordination, Inori escapes with Shu while Ayase, Tsugumi and Argo escape on their own and Arisa defends Gai, revealing he was the one who told her to start the coup and joins the Anti Bodies.

Mana has almost taken control of Inori's body and Gai tells his father, Shuichiro, that the Apocalypse will be coming and announces it to the world that the Leukocyte will destroy Earth on December 25th. The remnants of the Undertakers and the Kuhouin Group escape Japan on a ship along with the students of Tennouzu where Shibungi, who was released by Gai, gives Shu a journal by his father which reveals the Apocalypse virus history. In 2013, Shuichiro was a Professor researching on Genomic Resonance and befriended Shu's father Kurosu, who the latter was interested in the former's work. In 2017, Kurosu meet his future first wife, Saeko Shijou, a fellow colleague whom he marries after she became pregnant with their first child, Mana. But in 2022, a meteorite crashes on Earth and was discovered by Mana and Saeko. Shuichiro and Shu discovered a virus inside the meteorite which reacts when the Genomic Resonance was used.