Shuji and Chise start new life at a small port. They find jobs, and spend time together with the neighborhood happily. But her condition is getting worse.
Teenage boy Shuji got a cute girlfriend Chise recently. One day, unknown fighter aircrafts attack on a downtown where Shuji and his friends are doing their shopping. Then, Shuji has a bad feeling when he finds something red light in the sky.
Shuji and Chise plan to get away from here and live somewhere else by themselves. But there's no way the JSDF let her go. Shuji remembers his previous girlfriend Fuyumi while waiting for Chise at a station.
One week has passed since Sapporo was hit by the air raid. Chise confesses Shuji that JSDF transformed her into an ultimate weapon for the war, and she suffers from growing up her body as a weapon. But he finds it hard to accept the reality.
Shuji and Chise go on a date to an aquarium. After a while, Kawahara in JSDF picks her up. Shuji is upset, and then, goes to meet Fuyumi. Meanwhile, Chise gets to know Tetsu on the battlefield.
Shuji and Chise spend the last night together at the observatory. Finally, Doomsday has come. She promises him that she'll protect their hometown as much as possible, and flies into the sky.
Chise saved her hometown, but she suffers for something she has done. Shuji feels angry at himself for not being able to understand her. Meanwhile, Atsushi enlisted JSDF, he gets to know Tetsu.
A city also ceased to exist by Chise. After that, she tries to get back home. Meanwhile, JSDF decides to take over the high school building in her hometown.