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.

Tokyo, Winter. Despite the use of the Youth Ordinance Bill to enforce curfews for minors and regulate the use of the Internet, young people continue to fight for their own freedom through underground methods. One such group calls themselves Surat. They have decided to take on Fumito Nanahara, a man who has great influence on the political world, and basically controls Tokyo with an iron fist. While using the Internet as a weapon to discover more information about Fumito, they learn about "Tower", the secret organization behind Fumito which engages in human experimentation.

Takizawa prevented Japan's destruction - and then he vanished. Six months later, clues lead Saki to the Big Apple in search of her missing friend. Meanwhile, the remaining Selecao are plotting their final move. Some of them would prefer Takizawa dead and out of the way. Some might even be willing to help him achieve his goals. Unfortunately, some are prepared to destroy everything if it means claiming checkmate in Mr. Outside's puzzling game.

Accused of terrorism and feeling the heat, Saki's high-tech crew is in the crosshairs. Meanwhile, the shroud of mystery covering Takizawa is lifted as he and his fellow Selecao make their final moves. Every game must come to an end. For those playing Mr. Outside's twisted game of conspiracy thrills, the end comes now.