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.

At a press conference, the Superintendent-General makes himself a prime target for the Laughing Man's threat. Section 9 has gathered enough evidence to arrest Nanao=A, but before they can, he is able to release a modular, delayed-action virus. The virus seems to only affect those on the security detail that is guarding Superintendent-General Daidō. However, Section 9 will not know who on the security team has been taken over by the virus until the symptoms begin to manifest. By that time, it may be too late.

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.

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.

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.

Armed terrorists have taken over the Chinese Embassy in New Port City. Holding an unknown number of hostages, the group, calling themselves the Individual Eleven, are demanding that the government cease accepting Asian refugees and dissolve the five Asian refugee camps situated throughout Japan.

The members of Section 9 have mobilized and are in position to move in. However, due to the events of the Laughing Man Incident (1st GIG), Section 9 technically no longer exists. The unit must wait for an official order from Chief Aramaki, who is busy making his case in front of the new Prime Minister of Japan.

Section 9 has uncovered Shō Kawashima's ("FAKE FOOD") external memory device on the net. Hidden in a route to the Asian matrix only accessible through the European array, Section 9 concludes that the device was hidden by Gouda. Unfortunately, Gouda has left no trace of his movements in the device.

The Major prepares to dive into the device with Bōma and Ishikawa watching her closely. However, before she can dive, Aramaki notifies her that someone even more important than the external memory device has just surfaced...

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 Chief Cabinet Secretary uses the excuse of the refugees possessing 10kg of plutonium to mobilize the military against Dejima. With the available evidence against the refugees, Prime Minister Kayabuki reluctantly agrees. However, she soon learns from the Chief Cabinet Secretary that he's aligned himself with Imperial America and is now after her job.

Knowing her days as P.M. are numbered, she agrees with Aramaki's plan and calls the U.N. in for a nuclear inspection of Dejima. The move buys them some time to defuse the situation, and Section 9 heads to Dejima to meet up with the U.N in two days. However, with tensions running high it is only a matter of time before someone fires the first shot.

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.