To recap: Shuji and Chise are high school students. A war is going on and Chise has been made into a weapon by the Japanese army. She's now a cyborg and each time she goes into battle, she changes a little bit more, becoming even less human. In the last volume, Chise broke up with Shuji, saying they should just be friends.
Shuji and his friend, Atsushi, go on the roof to talk about Atsushi's crush on Akemi, the girl on the track team who has been Shuji's friend all his life. Atsushi asked Akemi out and she shot him down, so Atsushi has decided to join the SDF and take part in the war. Atsushi later comes by Shuji's house, and the two young men go for a walk. While they are out during the night, an squadron of fighter planes sails over the city. Before the boys can react, the planes are all destroyed.
Shuji and Atsushi split up and Shuji finds Chise in the streets. They kiss - very passionately - and Chise reminds him that they're friends and runs away.
At school, Akemi takes Shuji to task for breaking up with Chise. She and Chise have talked as well, and Chise explained what was going on. It appears to the reader that Akemi may have a crush on Shuji that she's never acted on based on her reactions to what Shuji and Chise both tell her.
The classes at the school continue to dwindle as kids stop attending. Atsushi joins the SDF only to hear rumors about a Captain Chise, wondering at how a captain has the same name as his best friend's girlfriend. He starts trying to find out about this captain, only to run into more and more dead ends.
Meanwhile, Chise has stopped going to school. Shuji hasn't seen her for some time. Chise has started spending time with Tetsu, who is a married soldier, part of her original company and the only one left alive. He more or less adopts Chise as his little sister, running off with her to the boarded up town to "buy" ramen noodles and clothes for Chise to wear, since the military refuses to supply any more (every time she goes into battle, she destroys her clothing).
The story ends with a cliffhanger that makes the reader want to continue reading to find out what happens with Shuji and Chise.