Shu returns to school with Inori since his arrest by the GHQ. Thanks to a cover story that he was interviewed by the GHQ for finding one of their cellphones and the student council president Arisa Kuhouin supporting Shu and defending him against malicious rumors, his classmates welcome him back with open arms. Shu also learns from his friends Hare Menjou and Souta Tamadate that Yahiro hasn't been back to school since his arrest. Later, Shu's mother Haruka comes back home and welcomes Inori living with them with open arms. Meanwhile, the Undertakers are running out of supplies and need a new supply route which Gai knows someone who will help them. The next night, Arisa and her grandfather, the head of the Kuhouin Group attend a party on a cruise ship where Shu and Gai have snucked in to make a deal with Arisa's grandfather. However, the Anti Bodies learn about the deal from an "informant" and sends Daryl, Segai and Rowan to work with GHQ Colonel Dan Eagleman whom the latter plans to shoot down the ship with Surface to Air missiles. After Gai flirts with Arisa and makes his business proposal with her grandfather, Shu learns from Tsugumi about the attack and tells Gai about it in order to save the passengers on the ship which include his mother. With Gai's help of bringing Arisa to the upper deck, Shu is able to extract her Void and use it to shield the ship from the missile which Colonel Eagleman orders his men to fire all of their missiles which are stopped thanks to Shu. With the threat over, Arisa's grandfather agrees to help supply the Undertakers which unaware to everyone but Gai and Shinbugi, Gai was the GHQ informant. Before leaving, Gai comments to Arisa despite the tough image she gives out, she is very shy when being doted on by others. As Shu and Inori leaves for school the next day, Shu admits to her that this is the first he was glad to use Voids while Haruka looks at a photo with her, her son Shu and the girl from Shu's memories.

Hare and Kanon notices how much Shu has changed and is more active. In order to help Hare get close with him, Kanon lies to Shu that Hare needs his help for her shopping. As Hare is about to confess to Shu on the train, Yahiro suddenly appears which Shu tell Hare to go shopping herself as he wants to talk with Yahiro. Yahiro brings Shu to his hideout where his brother, Jun is also staying and reveals that he and his brother have been on the run from the GHQ because they wanted to euthanize Jun. While Shu won't forgive Yahiro for betraying him, he will help Jun escape for Yahiro's sake and calls the Undertakers to pick them up. However, the GHQ have been following them and sends Seiga and Daryl. Cornered in a warehouse, Shu forcibly takes Yahiro's Void before telling Yahiro he will never betray his friends just like him. Daryl's Endlave arrives and fight Shu using a new weapon that targets his Void while Seiga watches. But when Jun stands up, the weapon target him instead. Suddenly, the crystals on Jun's body migrate to Daryl's Endlave and takes control of it and proceeds to attack the GHQ and Yahiro. Shu stabs the infected Endlave with Yahiro's Void and enters Jun memories where Jun himself shows Shu his and Yahiro's past before the "Lost Christmas" incident. Jun also reveals because of the crystals on his body, he could see people's true self including his brother, who while loves and cares about him, also hates him for burdening him as well. Wishing for his final memories of loving Yahiro and not hating him, Jun begs Shu to use Yahiro's Void to end his life before he kills Yahiro which Shu is forced to do so which Jun thanks him. With Jun's death, the infected Endlave breaks down while Seiga leaves. As Yahiro regains conscious and asks where Jun is, a mortified Shu confess to Yahiro that he killed him, unaware that both of them were followed by Hare.

While the virus is still spreading over Japan, Daryl arrives at the airport and kills everyone there in a rage of fury, including his own father Major General Yan. With the GHQ higherups gone, Shuichiro took over control of the entire military, and declares that the Funeral Parlor spreaded the disease as an act of terrorism. Meanwhile, after an call from Tsugumi, Shu finally regained control over himself. He then gathers Hare, Souta, Yahiro, Kanon, and Arisa, and explained to them that he wanted to go and rescue Gai and Inori. After witnessing Shu's power to draw out voids, the five students agreed to tag along. Back at the GHQ Headquarters, Haruka managed to escape from Shuichiro, but bumped into Inori and Gai. With Haruka's help, Inori was able to sing and broadcast her song "Departure" all over Japan. The song was able to reverse the effects of the Apocalypse Virus. At the same time, Shu and his friends arrives at the GHQ HQ, breaking through the barricades using different voids. When Shu finally reached Inori, a blond-haired boy appeared from behind and withdrew Inori's void, then sliced down on Shu. But Gai appeared and took the hit, saving Shu. The episode ends with Shu holding the unconscious Gai, while Shuichiro and Segai enters the Gate of Hell leading to Cocytus.

The students of Tennouzu work together to improve their environment by making use of their voids provided by Shu. However, the situation starts to deteriorate as the blockade draws closer and the supply of vaccines starts running low. Rumors about Yahiro's plan to prioritize the survival of those with stronger Voids with a Void Ranking system create turmoil among the students, despite Shu being opposed to the idea. Meanwhile Hare is encouraged by Tsugumi to confess her feeling to him, but at the sight of a troubled Shu who is questioning his leadership, she refrains herself and comforts him instead, telling he is a kind "King".

As the blockade gets closer to the school , causing fear amongst the students, Shu become more ruthless to maintain order. Yahiro warns him the students will hate him if he continues acting like this, but Shu insists it's necessary or they might end up dying like Hare. Arisa, traumatized after being attacked by Inori, is contacted by an unknown individual (later to be revealed as Segai), who convinces her to turn the students against Shu. Arisa seduces Hirohide and convinces him to secretly spread a rumor to the students that they will die if their Voids are destroyed and Shu is keeping it a secret, creating greater resentment against him.

Haruka opens a safe guarding the third and final Void Genome, but is stopped by Shuichiro, who is revealed to be her older brother. He confesses that he was the one who killed her husband, Shu's father, before shooting her, but she manages to escape with the Void regardless. An arrest warrant is issued on Haruka, Segai offers to lead the search for her. As she heads to the Kuhouin estate for shelter, her old friend Kurachi tells her the estate is no longer safe now that Okina is dead, and they head to an Undertakers hideout. Arisa is approached by Shu who convinces her to help him rescue Inori, as she wants to learn more about Gai's true intentions.