For years, Japan has been plagued by kaijuu, giant monsters wreaking havoc. To defend against them, the Defense Corps, an elite military unit, bravely safeguards civilians. After a kaijuu's defeat, sweepers from the Professional Kaijuu Cleaner Corporation handle the remains.
Kafka Hibino, a discontented 32-year-old sweeper, harbors dreams of joining the Defense Corps. Despite failed attempts, he settles for his mundane job. When spirited 18-year-old Leno Ichikawa joins his team, Kafka's aspirations resurface.
After a series of events and a fateful encounter with Leno, Kafka becomes infected by a parasite-type kaijuu, transforming him into a humanoid monster. Empowered by his new abilities, Kafka resolves to pursue his long-held dream once more.