On the last day of summer vacation, Naoyuki goes to school for intending to swim after his forty-day long trip with Kunihiro investigating the Sunohara base. At the school pool, he meets Iriya who in equal surprise falls into the shallow pool, thinking that she is drowning. Saving her and treating her subsequent nose bleed, he begins to teach her how to swim. He discovers silver circular caps on her wrists that she says taste like electricity A military siren interrupts them, and Enomoto appears, telling Naoyuki to leave first. Passing through the military blockade, he receives a bug planted in his the upper-right part of his neck. The next day, he Iriya appears at school as a transfer student. After the opening ceremony, an air raid drill alarm sounds, causing Iriya to take Naoyuki and run into the secured shelter under the impression that a real air raid was about to occur. Inside, after losing a game, Iriya collapses. While trying to treat her, he is caught in an awkward position when Shiina and some other open the shelter.

Kunihiro orders Naoyuki to have a date with Iriya. On Saturday, Iriya waits for him for four hours before the meeting time of 10:00. They go to see the movie which begins at 10:30 where Iriya falls alseep, followed by both Kunihiro with Yūko and Enomoto with his assistant. Noticing that they have tapped his listening device placed in Naoyuki's wallet, Kunihiro manages to catch a picture of Enomoto and his assistant as they flee after being discovered. The commotion causes Iriya to take Naoyuki and run. Disposing of the Kunihiro's bug, they continue to be chased by Kunihiro and Yūko, under the impression they are enemies. However once they manage to ditch the two, they stop by a park where Iriya recounts a tale of herself and four others at the Nevada base when the group decided investigated the crash site of one of one of the group. The next day, Naoyuki finds her application for the newspaper club in his footlocker.

The newspaper club prepares a painted wooden model of the Sunohara base with a UFO hovering over it for the school festival. Before a new mission, Naoyuki asks Iriya what she would like to do for the school who then replies that she would like to do whatever Naoyuki is doing. Enomoto asks Naoyuki to promise to perform the folk dance with Iriya. On the second day of the school festival, the day of the folk dance, Iriya calls Naoyuki on the school phone, telling him to come to the Rokubanayama Hill at the Self-Defense Force's old practice grounds at 18:45. There Iriya dances with him from her Black Manta.

Kunihiro leaves to investigate a large fire that erupts in the Sunohara base at night, leaving signs of his departure. The next day, Akiho challenges Iriya to gather information for the newspaper club so as not to be a burden to Naoyuki just before she makes daily call to Enomoto. Followed by a group of four friends including Naoyuki, they soon began food-eating competition as a symbolic competition of their love for Naoyuki, concluding with a three course meal of massive quantity called the Strong Man's Set Meal (鉄人定職 Tetsujin Teishoku?). Resting after they're battle at Akiho's house, they become friends when Enomoto arrives, angry for not being contancted at noon. She returns to school the next day with her hair platinum-blonde and extremely frail. Her vision begins to fail, and in the clocktower of the school, she begins to fountain blood from her mouth; Shiina saves her by sticking five syringes into her body. After finding out that she keeps his things as a charm, he vocalizes his doubts about Iriya's situation, earning him a beating from Shiina. After recovering from his bruises, he decides with Iriya to run away from Enomoto. After removing the bug placed in the right side of his neck, they began their escape.

After two days of fleeing south, Iriya and Naoyuki find shelter in the Narimasu Elementary School (成増小学校 Narimasu Shōgakkō?) where Iriya decides to adopt a cat who she names Kōchō (校長?). The next day, while Naoyuki is heading over to a convenience store to buy food and supplies, a ragged man goes to Narimasu Elementary after hearing of a rumour of white haired girl there at appearing night from workers at the same convenience store. Iriya fends him off failing to kill him, slashing his leg before he violates her, causing him to faint due to blood loss as he calls the police. As they run away in the rain, Naoyuki breaks from stress and orders Iriya to never show her face in front of him again. From the shock, Iriya slashes him and breaks. She loses her sense of the present and begins associating Naoyuki's face with that of different people that she has met. In order to take care, of her he decides to take her to his grandparents place. Due to her deluded state, Naoyuki finds out about her feelings for him, after which, she collapses. Bringing her to his grandparents place, he finds Enomoto waiting for him.

Enomoto takes Iriya back and treats her illness. Over a dinner of green ramen, Enomoto tells Naoyuki about the situation surrounding the secret war and Iriya's involvement in that war, announcing that the final battle takes place in three days, on October 26.