Mamoru Suzuhara is a quiet student in high school, fascinated by modern warfare. When he learns that his crush, Aya Chiyono, is leaving with her family in a week, he summons the confidence to ask her to run away with him. Along with four other classmates, they decide to set up a base in an old coal factory. However, they soon realize that they are not the only ones occupying the space. Based on the novel of the same name, Bokura no Nanokakan Sensou follows the story of the group of adolescents as they come of age and rebel against the adults, learning to confront their emotions and protect what they cherish.