Cyborg detective Batou is assigned to investigate a series of murders committed by gynoids—doll-like cyborgs, which all malfunctioned, killed, then self-destructed afterwards. The brains of the gynoids initialize in order to protect their manufacturer's software, but in one gynoid, which Batou himself neutralized, one file remains: a voice speaking the phrase "Help me."

A member of an elite paramilitary counter-terrorism unit becomes traumatized after witnessing the suicide bombing of a young girl and is forced to undergo retraining. However, unbeknownst to him, he becomes a key player in a dispute between rival police divisions, as he finds himself increasingly involved with the sister of the girl he saw die.

On June 19, 1948, the bodies of Japanese novelist and short-story writer Osamu Dazai and his lover Tomie Yamazaki are found drowned in the Tamagawa Canal in Tokyo. Osamu Dazai previously attempted to take his own life at least three other times. During the post war period, Osamu Dazai's reached the reached the height of his popularity and he became the literary voice for a "lost generation." After their bodies are found people wondered if Tomie Yamazaki was the cause of Osamu Dazai's death.