After a five-year wait, Chinese vice foreign minister Jin has been allowed access to the Kagoshima War Memorial in Japan. Jin is the first Chinese dignitary to be granted access to the site, but not everyone is happy with the decision, and before long a death threat is made against Jin. Elsewhere, Aramaki visits the grave of one of his deceased comrades, a Colonel in the GSDF. While at the cemetery, Aramaki encounters the Colonel’s daughter, who voices her concern over her brother Yu’s sudden behavioural changes. When Section 9 determines Yu to be the prime suspect in the assassination attempt, Kusanagi and Togusa are sent to apprehend him, but arrive too late to arrest Yu. Soon after, Aramaki receives a disturbing phone call from his dead friend, who has cheated death by merging his own ghost with his son's, and intends to avenge his wife's death during the war by assassinating Jin.

The episode was rated 7.73 from 139 votes.

A heavy-assault multiped tank runs amok under the control of an unknown hijacker.

The episode was rated 7.75 from 269 votes.

The Ministry of Home Affairs learns that Jenoma revolutionary leader Marcelo Jarti has been visiting Japan regularly every five months. Jarti is a drug trafficker and one of the world’s most wanted men, and has been targeted for assassination by commandos of the United States Delta Force and United Kingdom Special Air Service (SAS) a total of six times and has survived each of these attempts. When Jarti returns to Japan following the most recently failed assassination attempt, Section 9 is called in to follow him and determine why Jarti has been visiting their country. They discover that the real Jarti had died several months ago after using a ghost-dubbing device to create dozens of cybernetic clones of himself, and the Yakuza running the cloning facility had kept releasing duplicates to prevent the Jenoma government from learning of their national hero's death.

The episode was rated 7.76 from 178 votes.

Section 9 suspects that the police investigators handling the Laughing Man case are using their primary suspect, a former Serano Genomics programmer with a shady anti-corporate past named Ei Nanao, as a decoy to hide some form of higher-level corruption. Aramaki orders Section 9 to commence around the clock surveillance on Nanao in an attempt to catch him in the act, but the hacker is killed before he can be brought in for questioning. Elsewhere, Kusanagi meets with her friend Kurutan, a hospital nurse, to use her external memory device in an effort to learn more about The Laughing Man case. However, when the police Superintendent-General is set to give a speech about the Interceptor incident and the Laughing Man case, one of the officers present has his cyberbrain hacked by the Laughing Man. The Laughing Man demands that the Superintendent-General tell the truth, or he will be assassinated.

The episode was rated 7.81 from 193 votes.

Yamaguchi, an old friend of Togusa's and a police detective working in the Laughing Man task force, is murdered after he calls Togusa, requesting to see him concerning what Yamaguchi terms "suspicious internal activity" by superiors in the police department. At Yamaguchi's wake, Togusa is approached by Yamaguchi's wife, who delivers an envelope from him to Togusa that contain a series of strange photographs. Upon scrutinizing the photographs, Togusa realizes that none of them are taken using a camera. Continuing his investigation, Togusa interviews another detective in the Laughing Man task force, who coincidentally mentions that the task force is waiting to bug a primary suspect in the case with cybernetic surveillance devices called "interceptors". The interceptors allow constant audio and visual monitoring of the subject via their own senses. Togusa concludes that the Laughing Man task force members were bugged with these devices illegally for monitoring.

The episode was rated 7.86 from 224 votes.

The Superintendent-General's press conference quickly descends into chaos after the Laughing Man's assassination threat. Kusanagi suspects that the Laughing Man has inserted a virus into the police units assigned to guard the event. As Section 9 members struggle to evacuate the Superintendent-General to safety, the anti-virus team at HQ races to develop a vaccine to protect against it. However, random civilians begin joining in the assassination attempt as well, without any sort of external influence. After escorting the Superintendent-General to safety and apprehending all of the assassins, the police are left wondering about what caused dozens of completely unrelated people to attempt to murder a single man. After the immediate threat is averted, Aramaki orders Section 9 to open their own investigation into the Laughing Man case

The episode was rated 7.95 from 184 votes.

Marco Amoretti, a former American Imperial Navy Petty Officer turned serial killer, has arrived in Japan and for the last two months has murdered several women by slicing the skin off their torsos in the form of a T-shirt. American CIA officers have been dispatched to Japan, ostensibly to assist Section 9 in their effort to track down and apprehend Amoretti before he can strike again. When the CIA officers show no surprise at the developments in the case, Ishikawa hacks into the CIA database and learns that Amoretti was part of an American Empire commando team sent into the jungles of South America to conduct a covert operation aimed at breaking an enemy’s will to fight by using terror tactics, such as flaying civilians alive. Elsewhere, Batou — an ex-JGSDF Ranger who has seen first-hand the horrors of the CIA operation — resolves to stop Amoretti by any means necessary.

The episode was rated 7.96 from 152 votes.

After the events of "Portraitz", Togusa uses J. D. Salinger's The Catcher in the Rye as a starting point and develops a theory that the Laughing Man is after something published on paper. Togusa receives permission to check out a Ministry of Health, Labour, and Welfare (MHLW) records building and stumbles upon a key piece of evidence: a list of Cyberbrain Sclerosis patients treated with a secret medication, known as the Murai Vaccine, has disappeared from the MHLW. Togusa traces the missing list to a group called the Sunflower Society, where he learns that several prominent Japanese citizens have been secretly treated with the experimental medication. Elsewhere, the head of the Japanese DEA unit dispatches the Narcotics Suppression Squad to eliminate the members of the Sunflower Society and recover the missing list.

The episode was rated 8.03 from 142 votes.

Having learned the entire truth behind the Laughing Man Incident from the Laughing Man himself, and confirming the information with Serano, Section 9 is finally ready to make their move against the man behind the corporate terrorism: standing Secretary General Yakushima. However, 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. When Aramaki arrives to speak with the Prime Minister, he presents the incriminating evidence against Yakushima, expecting the Prime Minister to take action and remove Yakushima from office. However, the Lower House elections are entering a crucial stage, and without the support of his party in that House, the Prime Minister is uncertain of his ability to have Yakushima removed from office and arrested for his crimes.

The episode was rated 8.06 from 124 votes.

The Ministry of Health, Labour and Welfare's database has been hacked into, and classified material has been stolen. Section 9 traces the hack and determines that the hack job originated from a facility that helps people with Cyberbrain Closed Shell Syndrome. Togusa goes undercover to investigate the social welfare facility, and immediately encounters suspicious behaviour from the facility's supervisors. Togusa manages to learn that a person called "the Chief" visited the center during the week that the MHLW was hacked, but before he can determine the significance of this information Togusa is discovered; simultaneously, the facility's security system unexpectedly goes online, and Section 9’s databases are subsequently hacked, leading Kusanagi and Batou to make an emergency insertion to evacuate Togusa.

The episode was rated 8.13 from 148 votes.

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 are the remaining members of the Narcotics Suppression Squad. As Aramaki leaves the building he shares an elevator ride with former prime minister Kanzaki, who privately discloses that the prime suspect "pulling the strings" has a lot of friends in high places and strong connections to the navy. Elsewhere, the remaining members of the Narcotic Suppression Squad attempt to frame Aramaki with drug trafficking, concocting a story about his homeless brother to lure him to the refugee district and arrest him, but their plan fails when Batou rescues the chief before the police arrive on the scene. Meanwhile, Kusanagi seeks to repair her prosthetic body after incurring severe damage in a battle against the government's latest prototype power armor.

The episode was rated 8.13 from 136 votes.

The Laughing Man returns to kidnap Ernest Serano, the CEO of Serano Genomics, just as he did six years before. Returning to 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 about the Murai Vaccine, and in response Serano informs the Laughing Man that the whole time, he was under house arrest. Meanwhile, Section 9 determines the Secretary General Yakushima to be the man behind the Laughing Man scandal, and resolve to take Serano into protective custody to obtain his testimony. When the team discovers that Serano has been kidnapped by the Laughing Man again, they mount a frantic search to find and secure him.

The episode was rated 8.22 from 123 votes.

The dismantling of Section 9, spun by the media as a JSDF preemptive strike against a radical security unit planning a coup, provides the Prime Minister with the public support his party needs to win the Lower House elections. Immediately after the election, in keeping with his promise, the Prime Minister discloses the information regarding The Laughing Man case, fingering Yakushima as the ringleader. Three months pass, during which Togusa tries to come to terms with all that has happened with Section 9. In his attempts to find information on the rest of the team, he learns that the Major was killed and the remaining members of Section 9 are serving time in a state prison for high treason. The news upsets Togusa, and he resolves to assassinate the man responsible for Section 9's dissolution.

The episode was rated 8.29 from 127 votes.

Togusa finds himself in the hospital after being shot, but is desperate to impart what he has learned to the rest of the group. By diving into Togusa’s memories, Section 9 experiences the DEA raid against the Sunflower Society firsthand, prompting anger and rage. The Chief takes it upon himself to notify the head of the DEA of Togusa’s presence at the Sunflower Society building during the raid, prompting the DEA chief to order the Narcotics Suppression Squad (NSS) to the house of Dr. Hisashi Imakurusu. Dr. Imakurusu had overseen the board that denied the Murai Vaccine; after being diagnosed with Cyberbrain Sclerosis, he began using the vaccine in secret and subsequently went into hiding. Section 9 believes Dr. Imakurusu may hold a clue to unraveling the entire Laughing Man case, and undertake a desperate search to locate him.

The episode was rated 8.38 from 138 votes.

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's 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, but not before successfully dispersing information seeds given to them by the Major. With Batou and Kusanagi as the only uncaptured members of Section 9, Batou undertakes a risky sortie to the Major's apartment to recover her sentimentally-valued watch. Before he can escape, Umibozu commandos arrive and a firefight ensues. Batou successfully fends off the first wave of attacks, but is unexpectedly confronted with two armoured combat suits, the second of which proves to be more than he can handle.

The episode was rated 8.53 from 125 votes.