A gathering is initiated in cyberspace to discuss the Laughing Man. After a six year absence, the super-hacker reemerged from the shadows of the net and publicly threatened to assassinate Superintendent-General Daido of the Niihama Metropolitan Police ("INTERCEPTER"). With an audience watching across the net, several people take their places at a table in order to pass around their theories as to why the Laughing Man returned and to discuss what happened during the assassination attempt at the press conference ("DECOY" and "MEME").

After the events of "MACHINES DÉSIRANTES", the Tachikomas are sent back to the lab for further testing. Batou has little time to ponder the loss of his pet, however.

A foreign spy is suspected to be working within a Japanese Self-Defense Force training camp based in New Port City. With the Major and the Chief away at a security conference in England, Batou alone is assigned to go undercover to confirm the suspect.

Back on the Laughing Man case, Section 9 tries to find evidence of tampering in the Nanao=A case and delves more into the recent hack job at the Ministry of Health, Labour and Welfare ("PORTRAITZ"). Using J.D. Salinger's The Catcher in the Rye as a guide, Togusa checks out the MHLW and finds that something is missing: a ledger containing a list of vaccine recipients.

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.

A botched arms deal reveals that the government's plans to remove Plutonium from the Shinjuku dig site ("EXCAVATION") by sea have been compromised. Section 9 is called in to take the Plutonium out of Old Tōkyō by land.

The members of Section 9 are not happy being used by the government. Batou is especially incensed since Section 9 is supposed to be an offensive organization. His patience will be further tried when he and Section 9 find out who will be accompanying them on their mission...

Several bombings have occurred throughout New Port City. Each time, Section 9 arrives too late to stop their detonations. With a fifth and final bomb set to go off somewhere in the city, the unit puts all of the information they have found from the first four bombings together.

Even the Cabinet Intelligence Service is having their fair share of difficulties. A hacker has infiltrated its incredibly advanced computer security system. The hacker enters the vast array of information stored at the CIS and begins to collect data...

While on an assignment guarding the Prime Minister, Saitou and the Tachikomas pass the time playing poker with a few policemen who are also assigned to the case. Much to the chagrin of the other men, Saitou wins hand after hand.

The Tachikomas take notice of Saitou's uncanny accuracy and start to comment. Their constant chattering quickly gets on the other player's nerves, so to smooth things over Saitou recounts his time working as a sniper for mercenaries in Mexico.

Following a tip, the Major conducts an undercover investigation of Kuze in Taiwan. While there, she saves a boy running from the Mafia.

After being saved, the boy follows her, making sure that she finishes what she started. The mafia will continue to pursue the boy and the Major has to protect him.

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.