A certain type of android, the GA07_JL, nicknamed Jeri by its users, has been affected by a virus. Recently, all Jeri model androids have been committing "suicide".

Section 9 is called in as it may be related to a virus detected in an android at the National Assembly Building.

"Tachikoma Runaway": The Tachikoma that Batou has been feeding natural oil to awakens before the other Tachikomas do and leaves the hanger to have an adventure. On the town, it meets up with a girl named Miki who is searching for her dog.

"The Movie Director's Dream": While out on its adventure, Batou's Tachikoma found a cyberbrain that has something very interesting within it. One of Section 9's lab techs has become "lost" inside the device, and it's up to the Major to bring him back.

Recently, there have been numerous kidnappings which resemble the modus operandi of the Northern Territories Mafia. Aramaki and his team have been called in by the Prime Minister.

Ironically, the request to investigate the matter has come from the former Prime Minister of Japan, whose own daughter has been kidnapped by the Mafia. During his time as Head of Government, he had denied that the group ever existed. Delving further into the matter, Public Security discovers rumors that the abductors are harvesting organs and cyberbrains from the kidnapped children and selling them on the black market.

Events begin to shift into overdrive after the events of "ERASER". While things seem to be going Section 9's way, people in the shadows are starting to appear.

As Motoko, accompanied by her friend Kurutan, arrives at the hospital to switch to a new prosthetic body, Togusa begins the recovery process after being wounded by the DEA's NARC Squad. However, the people still active within the NARC Squad have a few more surprises in store.

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.

Kuze and the Major come up with a plan to save the refugees, but the chances of its success are slim. Realizing this, the Tachikomas disobey the Major's orders and come up with a plan of their own. Batou has also disobeyed the Major's orders to go to the bridge and is desperately searching for her in the ruins of Dejima. Meanwhile, the Prime Minister is frustrated with being spurned by the Chief Cabinet Secretary. Determined to be remembered as more than a mere figurehead, she takes matters into her own hands.