Major Kusanagi and Section 9 are called in to resolve a hostage crisis at a Geisha house staffed by android geisha. After the crisis is averted Aramaki is approached by a friend of his in the military who reveals that one of the hostages in the Geisha house was under investigation after requesting a report detailing military actions to be taken in the event of various states of emergency. Given the sensitive nature of the case, Section 9 is therefore asked to pick up the investigation where the original team left off.

The Head of the DEA is arrested for murder in connection with the raid at the Sunflower Society building. Aramaki orders Section 9 to go through all of the facility's records to determine who is pulling the strings behind the attacks against Section 9 and whether that person or group is responsible for orchestrating the Laughing Man incidents.

The Laughing Man returns to again kidnap the CEO of Serano Genomics, just as he did six years before. Returning to the scene of the café where Serano was first kidnapped, he and the Laughing Man share the story of the events leading up to the kidnapping and the events following it. During the conversation The Laughing Man asks Serano why he never fulfilled his promise to tell the truth.

Having learned the entire truth behind the Laughing Man Incident from the Laughing Man himself, and having confirmed the information with Mr. Serano, Section 9 is finally ready to make their move against the man behind the corporate terrorism: standing Secretary General Yakushima. Unfortunately, Yakushima has learned of Section 9’s planned move, and has leaked the existence of the group to the press in an effort to cast the organization in a bad light.

Aramaki has been released under his own recognizance, and meets with the head of the Ministry of Justice to explain the situation and ask for help in ensuring his team members safety, but the Minister of Justice is powerless to affect the situation beyond the prosecution of Yakushima. Elsewhere, Saito and Ishikawa are caught in separate traps set by Umibozu teams.

After 15 days of fierce fighting the Umibozu complete their operation to dismantle Section 9 by assassinating Kusanagi and capturing Batou. The dismantling of Section 9, spun by the media as a JSDF preemptive strike against a radical security unit, provides the prime minister with the public support his party needs to win the lower house elections. Three months pass, during which Togusa tries to come to terms with all that has happened with Section 9.

Two years have past since Section 9 was forcefully disbanded by the Umibozu. In that time Section 9’s members have regrouped, their headquarters have been reconstructed, and they have resumed their previous role as a special forces team that specializes in cyber warfare. Unfortunately, the team exists in a sort of "black hole": although the group has reformed they are operating without the consent of the Japanese government because the Special Forces Restriction Bill was used to dismantle the group.

Following nuclear World War III and non-nuclear World War IV (also referred to as the Second Vietnam War) Japan passed an act known as the Refugee Special Action Policy, inviting war refugees from all across Asia to enter Japan. Hundreds of Asian refugees took Japan up on the offer to enter their country, and have taken low wage jobs handed out to them by various companies looking for a low wage work force. Gino is one such refugee; having been involved in World War IV as a combat pilot, Gino has returned to Japan as a refugee.

A formal investigation into one Mr. Todoko has yielded evidence that he may be managing former Secretary General Yakushima’s assets. This prompts the government to launch its own investigation into the allegations, but there are two problems: Todoko’s vault is state-of-the-art; only he can access the assets in the vault. The other more immediate concern is that a hacker and thief by the name of Cash Eye plans on infiltrating the vault during an exclusive high-society party.

The largest live fire exercise ever conducted by the Japanese Self Defense Force is currently underway in advance of the Prime Minister’s planned announcement of the repealing of the Refugee Special Action Policy. As part of this exercise, a group of soldiers with Ground Self Defense Force have staged a 5:30 AM practice raid against a building where a simulated refugee terrorist group is alleged to be keeping a think tank.

Prime Minister Kayabuki has formally renounced the Refugee Special Action Policy, a move that has drawn much criticism from refugees all over Japan. While on a tour of the Dejima Island, a massive refugee population center, the Prime Minister receives an assassination threat, and Aramaki is summoned to Fukuoka to offer his insight into the threat. The cabinet wants Section 9 to protect the Prime Minister, a role the team reluctantly agrees to.

The prime suspect behind an attempt to blackmail the Ministry of Energy has turned up dead in Nihima City, ostensibly the victim of a tragic accident; however, a more thorough examination of the body turns up evidence of homicide. Togusa follows up on the death of the suspect, and obtains "photographic evidence" that the man had intended to use against the Ministry of Energy; however the film piece has been exposed to light, and subsequently turned completely black. Togusa discovers that the "photographic evidence" was not a photo but a radiation badge. Some one has authorized the excavation of a prewar relic, but who...and why?