At a geisha house, the female androids have gone out of control. They have taken hostage two members of a foreign body, the Minister of Foreign Affairs, the Minister's secretary, and the head of the Minister's Support Association.

The situation is complicated by a feud over authority between the police and the military. Section 9 Chief Aramaki lends a helping hand and brings in his unit to resolve the crisis.

A prototype multiped tank has destroyed two other prototypes and broken out of a testing facility. Section 9, employing its own smaller multiped, the Tachikomas, is brought in to stop it.

The hijacker is using the ID of the tank's designer who had recently died. Whoever is operating the tank, their motives are unknown. Section 9 has little time to figure out these two mysteries before the tank enters the urban area.

While tracking the New World Brigade, an anti-cyberization group, to an unused radiation scrubber facility off Okinawa, the Japanese Maritime Safety Agency took pictures that show Eka Tokura, the kidnapped daughter of a cyber-technology company CEO. However, the girl had been abducted over 16 years ago when she had been 10 years old. In the recent photos, she looks just as she did on the day she was taken.

For reasons unknown, contact with the Maritime Safety Agency's reconnaissance team has been lost. Section 9 heads to the facility to locate the unit and find out why Eka Tokura was there.

A cat thief named Cash Eye has infiltrated a building owned by Federation of Economic Organizations Chairman Tsutomu Tadokoro. The cat burglar made quick work of the top-notch security system and left a calling card on the Chairman's desk saying that Cash Eye will be infiltrating his vault during an upcoming party.

Albeit reluctant to get Section 9 involved, Aramaki has no choice but to assist Tadokoro. Prime Minister Kayabuki has requested that his unit go undercover in order to prevent the burglary.

Despite close scrutiny by the authorities, the Dejima refugees declare their independence. Kuze is suspected to be the mastermind behind this new resistance and Section 9 is sent to detain him.

The Major hacks into the refugee cyberbrain hub and easily locates Kuze. When the team rushes to capture him, however, they find themselves in the middle of a trap.

The city of Fukuoka is evacuated when a live nuclear bomb is found. With the Dejima Refugees targeted as the prime suspects, the government sends the Self-Defense Forces into the city.

Aramaki suspects the CIS's involvement in this latest incident is deeper then it appears. Batou is sent to gather more information from Gouda, but will he be able to hold his temper against the arrogant agent?