A prototype multiped tank has destroyed two other prototypes and broken out of a testing facility. Section 9, employing its own smaller multiped, the Tachikomas, is brought in to stop it.

The hijacker is using the ID of the tank's designer who had recently died. Whoever is operating the tank, their motives are unknown. Section 9 has little time to figure out these two mysteries before the tank enters the urban area.

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").

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.

A highway accident involving a large commercial truck has left a fully prostheticized man dead, his body torn apart from the impact. Togusa is summoned by Aramaki to delve deeper into the matter as the dead man had recently tried to blackmail the Energy Ministry.

The dead man's name was Kanji Kotan and he had recently arrived to Niihama by way of Tōkyō. Due to the rest of Section 9 guarding the Prime Minister ("INDUCTANCE"), Aramaki can only send Togusa, with a Tachikoma as protection, to dig up what he can about the man's recent activities before he died.

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...

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.