Mamoru Suzuhara is an introverted high school student who spends his free time reading up on modern warfare. Upon discovering that his crush, Aya Chiyono, is reluctantly moving away with her family next week, he musters enough courage to ask her to run away with him. Consequently, Mamoru, Aya, and four of their fellow classmates set out and camp in the abandoned Satomi Coal Factory. After enjoying themselves during their first day there, they come to the surprising conclusion that they may not be alone in the factory.

Bokura no Nanokakan Sensou, based on the novel of the same name, is a coming-of-age story about an act of rebellion that evolves into a full-out war against the adults. Meanwhile, the children struggle to open up about their feelings and protect what they hold dear.