Sanpei Hinomoto is a lonely fifth-grade boy who finds no kindness from anyone except the small animals and insects he secretly cares for. His classmates bully him, his teachers scold him, and his own family treats him with cold contempt, disappointed by his poor grades and withdrawn nature. His only refuge is a hidden spot near the garbage dump where he tends to stray creatures.

On the last day of school before spring break, Sanpei suddenly becomes violently ill in his room and vomits. Inside the mess he discovers a strange red caterpillar-like insect. When he picks it up, it stings his finger with a thorn. The next morning his body begins to swell and discolor. Over the following days his skin rots, his fingers and toes decay and fall off, and his limbs gradually separate from his torso. His parents, deciding he will not live long anyway, refuse to care for him and leave him locked in his room.

Eventually Sanpei sheds his ruined human shell and emerges as a large poisonous insect. His family, horrified, holds a funeral using his discarded human remains and later tries to poison him. They bury what they think is his dead body, but he survives underground, digs his way free, and leaves home in silence. He seeks comfort at his old hideout, but even the animals he once loved now fear and reject his new form. He wanders through forests and sewers, attacked and driven away by humans wherever he goes.

Cornered and alone, Sanpei begins to fight back. He discovers his new body is dangerously strong, and he takes revenge on the children who once tormented him, killing them one by one. The violence becomes a spiral: he starts to enjoy the killing, then attacks indiscriminately, and his human memories fade until he no longer remembers ever being a boy.

One day a familiar scent draws him to a house. Peering through the window, he sees his family eating dinner together. For a moment something old and sad stirs inside him, and tears fall from his insect eyes. Then the window slides open and his father raises a hunting rifle. Wounded and bleeding, the bug boy flees into the night and falls into a river, drifting slowly out toward the sea.