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.

Motoko is asked by her friend Kurutan to investigate a strange scenario. A six-year old girl's life was saved by an immediate heart transplant. When her parents tried to send their gratitude to the donor, the donor's parents filed a police report since they never gave permission for the donation.

What's more, the investigating officer has now been hospitalized after an accident. There is more to this case then meets the eye and Motoko and her colleagues must find out who's behind these apparent illegal organ donations.

A new sniper device is tested out, but is found to have flaws. While Section 9 attends a debriefing session on the fate of the sniping device, the Tachikomas themselves begin to worry that tomorrow they could be the ones that are scrapped. The Tachikomas of Section 9 unite and discuss the various issues dealing with them that have occurred within previous episodes. They worry that the Major does not appreciate them. At the same time, the Major is looking into the idea of proceeding without the Tachikomas at Section 9's side.

"Machine désirante (Desiring-Machine)" is one of the key concepts of Anti-Œdipus, written by contemporary French philosopher Gilles Deleuze.

After the events of "MACHINES DÉSIRANTES", the Tachikomas are sent back to the lab for further testing. Batou has little time to ponder the loss of his pet, however.

A foreign spy is suspected to be working within a Japanese Self-Defense Force training camp based in New Port City. With the Major and the Chief away at a security conference in England, Batou alone is assigned to go undercover to confirm the suspect.

Post Traumatic Stress Disorder is put on full display. A Japanese National named Gino, who suffered through the horrors of Non-Nuclear World War IV, the Second Vietnam War, now passes his days as a helicopter pilot for the chairman of a media conglomerate. His cushy job, however, does not take away the sheer internal pain that Gino is facing.

As he moves through his isolated existence, Gino leaps between reality and fantasy. However, he keeps his dementia solely to himself. Having no one to help him, his condition continues to worsen.

While Ishikawa begins to dig deeper into the background of CIS Representative Kazunoto Gouda, the rest of Section 9 are instructed to arrest one Shou Kawashima, a Taiwanese vegetarian restaurant chef who has been seen at three locations where the Individual Eleven have claimed responsibility for attacking.

The Taiwanese restaurant where he works is near the Nanyou Shimbun (Newspaper) building that had received an earlier threat against it by the Individual Eleven. Section 9 moves into position around the Taiwanese restaurant and commences their stakeout.

With the latest Individual 11 incident still fresh in the public's mind, Section 9 discovers that only a skilled face sculptor could have created Kuze's prosthetic face. Since only two artists fit that description, they quickly locate the craftsmen and go to question them.

Following a tip, the Major conducts an undercover investigation of Kuze in Taiwan. While there, she saves a boy running from the Mafia.

After being saved, the boy follows her, making sure that she finishes what she started. The mafia will continue to pursue the boy and the Major has to protect him.

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?

As the attack on Dejima escalates, the Major catches up with Kuze. She explains the whole situation to him and he agrees to follow her. They are about to leave when both are attacked by the Self-Defense forces and in the confusion are trapped under the rubble.

Togusa rescues the Prime Minister and brings her back to her office. There, Aramaki hopes her influence will stop the launching of the ultimate weapon. Meanwhile, Batou reasons with Section 4.