Takao, who is training to become a shoemaker, skipped school and is sketching shoes in a Japanese-style garden. He meets a mysterious woman, Yukino, who is older than him. Then, without arranging the times, the two start to see each other again and again, but only on rainy days. They deepen their relationship and open up to each other. But the end of the rainy season soon approaches …

The story is set in 2027, one year after the end of the fourth non-nuclear war. New Port City is still reeling from the war’s aftermath when it suffers a bombing caused by a self-propelled mine. Then, a military member implicated in arms-dealing bribes is gunned down. During the investigation, Public Security Section’s Daisuke Aramaki encounters Motoko Kusanagi, the cyborg, wizard-level hacker assigned to the military’s 501st Secret Unit. Batou, a man with the “eye that does not sleep,” suspects that Kusanagi is the one behind the bombing. The Niihama Prefectural Police detective Togusa is pursuing his own dual cases of the shooting death and a prostitute’s murder. Motoko herself is being watched by the 501st Secret Unit’s head Kurutsu and cyborg agents.