Bizarre creatures referred to as "Unknown" appear over the coast of Tokyo Bay. Defending against them is the mission of high school students in Tokyo, Kanagawa, and Chiba who possess a supernatural power known as "World." Among them all, the head of the Tokyo school, Ichiya Suzaku, defeats Unknown with particularly overwhelming power, but Tokyo's subhead, Canaria Utara, observes his lack of teamwork with a troubled expression.

Rumors are swirling among students repairing the half-destroyed Aqua Line that an Unknown has appeared in the area. The representatives of each city divide into two teams to investigate, and Suzaku ends up on a team with Hotaru as well as Kasumi, one of his least favorite people.

Some of the students are about to be transferred to a safer location, and Ichiya skips patrol duty to visit one such student in the hospital. In Ichiya's opinion, all the students being transferred are "inept amateurs." Meanwhile, in Ichiya's absence, a colossally huge new type of Unknown appears.

Canary was injured in the battle against the giant Unknown, leaving Suzaku in a desperate situation. After being saved by the Chiba and Kanagawa forces and beating a retreat, Suzaku is called out by Administration to take responsibility for acting on his own, but he pleads for a chance to finish the battle with the help of Chiba and Kanagawa.

The casualties caused by the Unknown's sudden attack are so severe, the students of each city can't conceal their shock. Suzaku loses his confidence and will to fight, so Maihime steps up to act as Tokyo's leader. Maihime is strong and encouraging when she stands before the students of Tokyo, but...

Hotaru engages in battle with a new type of Unknown in the no-entry zone, while Suzaku fights a desperate battle at Umihotaru, where the Chiba team have taken him. At the same time, an unprecedented number of Unknown appear in the sky above Tokyo. In the face of the calamity befalling them, Maihime takes the hope of the world upon her own shoulders.

Hotaru races toward Tokyo, determined to keep her promise to never keep Maihime waiting again. Meanwhile, Maihime is increasingly overcome with exhaustion as countless Unknown bear down on her. Just then, a unique Unknown that Maihime determines to be their boss shows up.

After the heavy losses suffered by the Kanagawa camp, Chief Medical Officer Okuni suggests pulling the defense line back to prioritize the protection of the Japanese mainland. But she insists that this would necessitate the reassignment of Asuha, their strongest remaining battle asset, to the interior, and Kasumi is not willing to let his sister go so easily. When Okuni responds to Kasumi's refusal by inviting him over for a private chat, he assumes her goal is to persuade him to change his mind, but Okuni's true objective lies elsewhere...

As his eyes begin to see the true nature of this world, Kasumi entrusts Asuha with the city's defense and begins his own investigation. Asuha, now the central pillar of all three cities' defense, attempts to improve the lethargic Suzaku's mood in an effort to enlist his aid... but then an Unknown attack alert is sounded.

After finally learning that reality is not at all what he thought it was, Suzaku is too stunned to grasp the situation. Asuha is still struggling to comprehend what's going on in their world, as well. Then Kasumi shows up, along with a woman who calls herself Kasumi and Asuha's mother...

The humans launch an all-out attack on the Unknown's base in order to take back the gate that links the human world to that of the Unknown. However, while some of the students from the combat curriculum are prepared to fight, other students' feelings about the battle are more complicated. What decision will Suzaku make?