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.

A high-level hacking has occured at the Ministry of Health, Labour and Welfare. Section 9 has traced the source of the hack job back to a vocational aid center located high in the mountains.

The hack was done by someone very skilled since it only took two hours to crack the MHLW's ultra-secure barriers. The odd thing is that the MHLW has not filed a formal complaint about the incident. Togusa is sent undercover to discover what is going on at the aid center.

Acting on a tip, Section 9 breaks up a cabal of thieves hell-bent on wrecking a Japanese financial institution. Shortly after the raid a Chinese intelligence official contacts Section 9 and informs them of suspicious activity that he believes may indicate an assassination attempt by Chinese Socialists on a prominent, yet reclusive, Japanese multi-millionaire.

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.

As the JMSDF's Special Forces Unit rounds up the remaining members of Section 9, Daisuke Aramaki meets with the Minister of Justice to make one last appeal to the government to salvage his team.

Section 9 may be down, but certainly not out. They have help in the form of their "think-tanks", otherwise known as the Tachikomas. Public Security will make one final push to save itself from extinction.

Togusa has been released from jail, but his badge and gun are confiscated and he is given papers showing the dissolution of Section 9. Out of work and depressed, he tries to find information on the others, but turns up nothing.

Trying to turn his life around, he begins to look for a new job, only to be sidetracked by the ongoing case against Secretary-General Yakushima involving the illegal use of micromachines. With the news plastered everywhere, Togusa cannot help but wonder where he stands now.

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.

During a scheduled maintenance, the Tachikomas begin to chat away about the Individual Eleven.

While talking in their new "forum", Batou and Togusa appear and take one of the Tachikomas - who just happens to be Batou's pet - with them to Spring-8 to look at the scientific evidence gathered on the Individual Eleven.

Section 9 heads to Etorofu in search of Kuze. During their investigations, the Major finds an interesting floppy disk on the body of a dead addict.

The floppy proves to be a goldmine of information, as it contains records of plutonium transactions. The last buyer to purchase the material was a group of Asian refugees. Realizing the transaction is about to take place, the team rushes to the location and is surprised by what they find.

With the felling of Dejima Bridge by the refugees, a rumor circulates around the Cabinet that the refugees plan a mass suicide bombing using nuclear bombs. Fearing this, the Cabinet steps up the attack against the city. Meanwhile, Prime Minister Kayabuki has been secretly arrested and taken to an unknown location. Aramaki, Togusa and Proto, in trying to help the P.M. are also taken into custody and secured in her office.

With Section 9 having entered the non-communication zone and Aramaki being cut off from communication, Ishikawa and a Tachikoma make their way to Spring-8 on their own. Meanwhile, Gouda has sent an unwitting Section 4 after Section 9 to retrieve the plutonium.

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.