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").

Marco Amoretti, a former Navy Petty Officer from the American Empire, has come to Japan and is committing heinous acts of brutality against women.

Section 9 is assisted in this matter by the American Empire's CIA. While this doesn't sit well with Public Security's members, Batou finds the whole case particularly hard on his psyche as the nightmares from his past rear their ugly head.

Acting on a tip, Section 9 breaks up a cabal of thieves hell-bent on wrecking a Japanese financial institution. Shortly after the raid a Chinese intelligence official contacts Section 9 and informs them of suspicious activity that he believes may indicate an assassination attempt by Chinese Socialists on a prominent, yet reclusive, Japanese multi-millionaire.

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.

The Laughing Man returns and, just as he did six years ago, kidnaps the President of Serano Genomics without being detected. Section 9 arrives too late and sets out to find him.

Meanwhile, the Laughing Man and Mr. Serano discuss what happened six years ago. The stakes are much higher this time, and for the Laughing Man failure is not an option.

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.

During a visit to the Dejima Refugee Residential District off the coast of Nagasaki, Prime Minister Kayabuki receives a bouquet of flowers that is accompanied by an envelope stamped with the diamond seal seen in "NATURAL ENEMY". The envelope contains a letter that promises an attempt to take the Prime Minister's life.

At a meeting of the Prime Minister's Cabinet, Aramaki is shown the letter and told that so far the stamp on the envelope has turned up in eight other terrorist incidents. The Cabinet calls for Section 9's assistance. However, much to the unit members' chagrin, Section 9 will not be deployed in an offensive role.

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.

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.

Section 9 heads to Etorofu in search of Kuze. During their investigations, the Major finds an interesting floppy disk on the body of a dead addict.

The floppy proves to be a goldmine of information, as it contains records of plutonium transactions. The last buyer to purchase the material was a group of Asian refugees. Realizing the transaction is about to take place, the team rushes to the location and is surprised by what they find.

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.