When Suzaku and the others stormed the gate, they found themselves face-to-face with someone they never expected... one who, despite being human, doesn't fall on the same side as the world they must protect and the people they must save. Suzaku and the others are forced to question whether they're truly prepared to do what they came to do. The battle for the world will be settled here and now...
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...
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.
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...
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.
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.
The story takes place in a world where people continue their war against the "unknown"—the enemy of humanity. Children who have been evacuated to a cold sleep facility during the invasion by the "unknown" several decades ago wake up from their slumber and learn that their bodies developed some supernatural forces. In order to protect the country from the "unknown" emerging from the Tokyo bay gate, the boys and girls wage battles in the defense the cities of Tokyo, Kanagawa, and Chiba.