At the end of the twenty-first century, a rare disease named "Cagaster" began infecting the human race — transforming them into massive insects. Two-thirds of Earth's population had been devoured by these insects before humanity came to a decision: those that were infected must be exterminated.

In the year 2125 — thirty years after the discovery of Cagaster — a young exterminator named Kidou finds a man dying from insect-inflicted wounds at the edge of the desert near the insects' "cage". The dying man entrusts Kidou with his daughter, Ilie, and tells him to seek out the girl's mother.