Kōta Hayano is a teenage boy drafted into the Japanese navy during World War II at approximately 15 to 16 years of age. Initially training as a pilot on a trajectory implying eventual kamikaze duty, he proves inept in flight and is reassigned to coastal defense submarine duty. He serves aboard a small, fictional submarine roughly 30 meters long with a crew of five, distinct from historical Japanese submarine classifications. Within this confined setting, Kōta encounters a large male sei whale, approximately 20 meters long, whom he names Kusuke.

Kōta harbors a romantic interest in a girl named Yoshie back home. He experiences a growing internal conflict between the military ideology demanding self-sacrifice for the empire and his personal desires, which include forming a bond with the whale and surviving the war to return home. His interactions with Kusuke are marked by friendship and curiosity, contrasting with the whale's persistent, comedic misinterpretation of the submarine as a potential mate.

Kōta's journey depicts a progression from adherence to military indoctrination toward personal awareness shaped by his experiences. The escalating threat from American anti-submarine forces, drawn by Kusuke's attentions toward the submarine, forces a direct confrontation between his duty and his connection to the whale. This culminates in a somber resolution reflecting the broader costs of war on individuals and unintended bystanders. Kōta serves as the primary human perspective through which the narrative explores the consequences of war and the unintended intersections between military operations and the natural world.