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.

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.

Togusa, at the request of Chief Aramaki, returns to work. Both head out to the Prime Minister's residence with a detailed report citing Secretary-General Yakushima as the real power behind the Laughing Man Incident.

However, before they can even leave their own building, they are told by the Minister of Home Affairs that Public Security has already been accused of being the masterminds behind the Laughing Man. The situation has gone from bad to worse and it will take a concerted effort by all of its members for Section 9 to clear itself of the charges.

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...

Ishikawa returns from the Peninsula with the latest intel on Kuze, but is surprised to learn of a possible refugee uprising. The Major and Aramaki are sent to see the Prime Minister to discuss this matter and the existence of "hub cyberbrains". While they wait, the rest of the team listens to Ishikawa's report on Kuze's past.

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.