The female android servants at a geisha house have gone out of control, taking as their hostages the Minister of Foreign Affairs, the Minister's secretary, the head of the Minister's Support Association, and three members of a North American business alliance. The situation is complicated by a feud over authority between the police and the military. Section 9 Chief Aramaki lends a helping hand and brings in his unit to resolve the crisis.
During a test run of a new tank, one of the prototype multipeds goes rogue. Escaping the facility, it heads for the urban area of Niihama. Since the tank's driver is unknown, as are their motives, Section 9 is quickly mobilized to deal with the threat. Using their own multipeds, the Tachikomas, the Major and her unit move in to make sure the tank driver and his deadly weapon do not make it to Niihama.
Several androids have recently been employing various methods of self-termination. Coincidentally, all the androids are of the same model: The Genesis Andross GA_07JL or Jeri. Since a similar incident has occurred at the National Assembly Building with an android translator, Section 9 has been called in to assess the threat. The Major and Aramaki begin their investigation, with the help of a Tachikoma, by visiting the plant where the Jeris were produced.
A former colleague of Togusa contacts him to ask for help with a case he has been working on. Unfortunately, before his colleague can meet with Togusa, his car plunges off of a road and explodes. Togusa is suspicious of the death because his colleague had been part of the special unit at police headquarters assigned to the Laughing Man investigation. Since it is a high profile case, Togusa is sure that his colleague's death was no accident.
With the recent death threat on the Superintendent-General's life that had been aired during a press conference about the illegal use of intercepters, Section 9 steps up their own investigation into the Laughing Man Incident. Aramaki briefs his team on a man named Nanao=A who has for some time been at the center of the investigation by the Laughing Man Unit at police headquarters. The Chief assigns Batou and Togusa to keep tabs on the man while he has the rest of the team dig deeper into Nanao's background to see if he is really the Laughing Man.
Section 9 attempts to arrest Nanao, but the room they had thought that Nanao was in turns out to be a dummy room. As they realize this, Nanao releases a modular, delayed action virus just as a press conference with the Superintendent-General is about to begin. The Major along with Satiou and Pazu are at the conference to make sure that the Laughing Man does not make good on his threat to kill the Superintendent-General. With the virus being able to manifest at the last possible minute, the Major and her team have their work cut out for them.
The Ministry of Foreign Affairs asks Section 9 to help them with a strange case. Marcelo Jiarti, a South American revolutionary leader, has had several attempts made on his life by such units as the U.S. Delta Force and the British SAS. However, he has survived each of these assassination attempts. For reasons unknown, Jiarti regularly visits Japan about once every five months for a total of twelve times in the past five years. The Ministry has requested that Section 9 surveil Jiarti and discover why the revolutionary enters the country so often.
Motoko’s friend Kurutan, who works as a nurse in a hospital, asks her to help her sort out a tricky situation. One of Kurutan's charges is a little girl, who needed a new heart. The girl, Moe, was fortunate enough to receive a new heart from a donor instead of a mechanical one. For the little girl and her parents, it all seemed to good to be true. Unfortunately, it is too good to be true.
Japan is once again transfixed with the recent reemergence of the Laughing Man after a six-year absence. With so much to talk about and little facts to go on, virtual chat rooms are abuzz with gossip. In one particular chat room, several people have stepped forward to air their opinions. As they begin, another participant appears. Forming herself out of digital information, she takes a chair at the virtual round table and listens in on the intense discussion to figure out the Laughing Man's identity and the reason why he has returned to the forefront.
Several female bodies have been discovered with their torso skin cut off in the form of a t-shirt. The suspected murderer is a former American sailor named Marco Amoretti. Section 9 learned the suspect's name through the American Empire's CIA. While they investigate the case, Section 9 must allow two CIA agents to take part in the hunt for Marco.
A high-level hack job has been instigated upon the Ministry of Health, Labour, and Welfare (MHLW). Breaching a huge array of defenses, the hacker needed less than two hours to break in and find what they were looking for. Luckily, their tracks were not concealed. The electronic trail leads to a Vocational Aid Centre within a mountainous region. However, the MHLW has not filed a police report on the matter. Section 9 Chief Aramaki sends Togusa on an undercover mission to gather info on the centre.
In the storage hangar at Section 9, Batou's Tachikoma starts up on its own. The Tachikoma realises that the natural oil that Batou had been giving it has altered its program since all the other Tachikomas only received synthetic oil. Opening the hangar's bay door, it takes a journey into New Port City. There, it encounters a girl named Miki who is looking for her dog. Unbeknownst to the Tachikoma, someone is watching its actions from the roofs of the city.
The Japanese Coast Guard photographs Eka Tokura, a girl that had gone missing sixteen years ago, with the New World Brigade as they kept tabs on the anti-cyberisation group. Eka had volunteered to become cyberised to promote her father's technology. Shortly after, the New World Brigade kidnapped her. However, the recent pictures of Eka show a girl who looks exactly like Eka did on the day she was kidnapped sixteen years ago.
Alerted to the threat of a robbery on a financial institution by a South China mafia group, Section 9 stakes out the group's hideout in a Chinese restaurant. Posing as garbage collectors, the Major and her team move in to arrest the group before they make good on their plans.
Saitou tests out a new sniping device during a field exercise. Unfortunately, the device fails to make the grade. After the exercise is completed, the members of Section 9 hold a briefing session to discuss the device's usefulness. During the briefing, the Tachikomas take a look at the sniping device themselves. Finding that the problem with the device lies with its Artificial Intelligence, the Tachikomas hold their own briefing session. Worried about the Major's feelings towards them, the Tachikomas wonder if they have become too smart for their own good.
The Tachikomas have been returned to the lab for further study. Unfortunately for Batou, he will have little time to think about the loss of his pet. While away at a Security Conference in London with the Major, Chief Aramaki sends Batou orders to investigate one Pavlo Zaitsev. A Russian-born former boxing champ, and someone that Batou has looked up to, Zaitsev has been suspected of spying on Japan while working as a trainer for the Japanese Self-Defence Army.
After attending a Security Conference in London with the Major, Aramaki goes to a bank to visit an old friend who had emigrated to England to manage a wine fund. While he visits with his friend, he allows the Major a bit of free time to walk the streets of London. Before they catch up on old times, Aramaki's friend relates to him her suspicions of possible illegal activity within the bank. As she voices her concerns, two mafia hit men prepare to break into the bank.
A Chinese dignitary has arrived in Kagoshima, a city on the southern tip of Japan, to attend a memorial service for Chinese war dead interred there. Protesters have staked out the area, and are making sure that their voices will be heard. At the behest of the Chinese Public Security representative, Aramaki mobilizes his team to provide security for the dignitary. Covering all the angles, they come to learn that an attempt on the dignitary's life is imminent.
Over the course of several days, a large number of girls have been kidnapped. All indications point to the Northern Territories Mafia. Employing a trick known as Blindfold Ivan, the mafia is able to kidnap the girls in broad daylight with no one witnessing the abduction. Unfortunately for the mafia, they have kidnapped the daughter of the former Prime Minister of Japan, who has always publicly denied the existence of the Northern Territories Mafia. Feeling betrayed, he requests help from the Home Affairs Minister, who calls in Section 9 to assist.
Back on the trail of the Laughing Man, Togusa uses his investigative skills to bridge the gap between what Section 9 knows and what they don't know. After his recent failure to find the culprit of the hack job perpetrated at the Ministry of Health, Labour, and Welfare ("PORTRAITZ"), Togusa is more determined than ever to bring all the facts to light. Using J.D. Salinger's The Catcher in the Rye to help with clues given by the Laughing Man, Togusa stumbles upon an event that took place several years before the infamous Laughing Man Incident. Digging further, he comes across information vital to the case.
Togusa had been shot in the chest by the DEA's Narcotic Suppression Squad, but managed to send a distress call, which is answered. At the hospital, just before he is put under sedation to be operated on, the memories in his cyberbrain are retrieved so the rest of Section 9 can view the events that led up to Togusa's encounter with the NARC Squad. Upon learning what Togusa uncovered, Section 9 moves to find Hisashi Imakurusu, who has pertinent information about a massive cover-up. Time is of the essence as the NARC Squad is also on the trail of Imakurusu.
The arrest of the NARC Squad members allows Section 9 to move in to arrest MHLW Bureau Chief Niimi. With Imakurusu dead, Niimi is the lead that Section 9 needs to crack the case. However, several well-trained NARC Squad members still remain to be dealt with. While Motoko goes to the hospital to be fitted with a new prosthetic body, Aramaki is presented with some very troubling news.
Bureau Chief Niimi has committed cyberbrain suicide, leaving Section 9 once again with no credible lead. Aramaki now decides to work on the last link to the Laughing Man Incident: Ernest Serano, CEO of Serano Genomics and the man who was kidnapped by the Laughing Man six years ago. During the past six years, Serano has continued to run his company under the protection of the Niihama Metropolitan Police. Aramaki makes an appointment to meet with Serano, but, before the interview can take place, Serano is once again kidnapped by the Laughing Man.
With all the evidence they need, Aramaki and a healthy Togusa head over to the Prime Minister's residence with enough proof to bring down the man who has pulled the strings from the shadows: Secretary-General Kaoru Yakushima. However, before they can even leave the building, the Home Affairs Minister tells Aramaki that Section 9 is suspected of being the group behind the kidnapping of Ernest Serano. Those in high places, once again, conspire to move against Section 9.
Section 9 is no more. Having disbanded the unit, the Major scatters her troops to the wind. They are all wanted criminals, hunted by the elite Special Forces unit known as the Umibouzu who will stop at nothing until every member of Section 9 is apprehended. Aramaki meets with the Minister of Justice to make his case for his unit to be brought back. Meanwhile, the remaining members of Section 9 make their final stand..
Arrested, relentlessly questioned, and then mysteriously released, Togusa has returned home to stew. He is no longer a member of Section 9 and his record has been cleared to show that he is a security guard who has been put on indefinite leave. Having been told to wait for orders from his superiors, but not knowing when those instructions will come, and not about to sit idly while he is blind to the truth, Togusa begins to examine the fate of Section 9 and its members.
Terrorists have taken over the Chinese Embassy in New Port City. The Prefectural Police have their SWAT team in position and are in the process of gathering intel on the terrorists. At street level, Section 9's undercover van rolls up to the building that houses the Embassy. Due to the Laughing Man Incident, the Unit had technically been disbanded. However, with Aramaki making his case for his team in front of the new Prime Minister, that is about to change.
Gino is a Japanese National who survived the horrors of World War IV, the Second Vietnam War. Returning to his country, he takes a job as the helicopter pilot/chauffeur for the chairman of a large media conglomerate. The war has had its affects on Gino's psyche. His perspective of the world has been altered for the worst as he has begun to have ideas about resetting the world. It is at this time that Gino meets an unlikely beauty in a world of eternal pain.
Infiltrating the Tadokoro Building with ease, a cat burglar named CASH EYE leaves her calling card on Chairman Tadokoro's desk. Written on the card is a thread to rob the powerful man during a very important social gathering. At the Prime Minister's request, and much to his chagrin, Aramaki readies his team to make sure that CASH EYE does not succeed in her heist. With his team in place, all that is needed now is their guest of honour.
While operating a helicopter during a joint training exercise between the Japanese Army and Navy over the sealed sector of the Niihama Refugee District, a pilot suffers a heart attack, which instantly kills him. The helicopter's Artificial Intelligence takes control of the helicopter and proceeds to hack into its sister ships. Having taken over ten other helicopters, which include one designed for refueling, the AI leads the deadly weapons to the radio tower in the Refugee District. Aramaki quickly mobilizes his team so that no harm will come to the refugees. While meeting with Kubota, his contact at the Ministry of Defence, he is approached by an intelligence operative named Kazunoto Gouda, who has a request to make...
Visiting the Refugee District on the island of Dejima, just off of the coast of Nagasaki, Prime Minister Kayabuki receives a death threat by the Refugee Liberation Organisation. On the card is the symbol last seen being planted in the dead pilot's house ("NATURAL ENEMY"). Aramaki is summoned to the Prime Minister's residence to be briefed on the situation. There, he is told that Section 9 will be acting as protection for the Prime Minister while others examine the death threat.
Togusa accompanies the Chief to investigate a freak accident that has left a man with a cybernetic body ripped apart. It so happens that the man had been at the center of an investigation into the blackmailing of the Energy Ministry. A tip from a reporter places the man's last known place of residence as the Shinjuku Ward of Tōkyō. While the other Section 9 members continue to pull security detail for the Prime Minster, Togusa is ordered by Aramaki to head to Tōkyō and find out the dead man's last known movements.
While Togusa is still trying to piece together the events that occurred in the Shinjuku Ward of Tōkyō from the previous episode, the Prime Minister summons Aramaki. He is briefed by Kayabuki about a batch of Plutonium that is to be transported out of an underground facility in the Shinjuku Ward, and told that Section 9 is to handle the transport. The other members of Section 9 are not happy about this, particularly Batou. He sees the Prime Minister's requests as interfering with the mission of Section 9. Carrying out their orders to transport the Plutonium goes from bad to worse when they are told that they have a guest who will be accompanying them...
After the events of the previous episode, the Major has Ishikawa do a thorough background check on CIS Agent Kazunoto Gouda. While Ishikawa digs into Gouda's past, Aramaki briefs Section 9 on their next mission. The Chief has obtained evidence of a man named Shou Kawashima who has been picked up on camera at many of the bombings by the Individual Eleven. He is a cook at a Taiwanese Vegetarian restaurant, but has not been seen there for several days. Aramaki assigns his team to stake out the restaurant, and if Kawashima appears, he orders Section 9 to arrest the man.
After issuing a warning to detonate five bombs within Niihama, an unknown group has set off four of those bombs, killing and wounding many bystanders. In each of the four instances, Section 9 arrives to late. The fifth bomb will go off soon, and Section 9 sans the Major are working non-stop to make sure there is no fifth explosion. Meanwhile, at the Central Intelligent Service Building, a master hacker has infiltrated the CIS's server. Making short work of its defence barriers, the hacker opens some secret files.
Togusa aids a woman who has been chased by a man through the streets of Niihama. With his Mateba, Togusa is able to disable the man's prosthetic body. Unfortunately, he does not secure the man's pistol. When Togusa helps the woman up, the man has enough movement left in his body to aim his gun and fire at the woman, killing her instantly. The murderer is brought to trial. However, due to the events that occurred immediately following the murder, Togusa is brutally cross-examined by the murderer's lawyer.
Training has commenced to find new recruits for Section 9. With Motoko acting as the target, Batou and Togusa watch as the recruits try to keep up with the Major. After ditching some of the recruits, Motoko has to lose just one more pair. She ascends some stairs in an alley and the recruits follow her. Moving out into the street above, the recruits see that they have lost the target. However, Batou and Togusa have lost contact with the Major as well.
Section 9 has uncovered Shou Kawashima's ("FAKE FOOD") external memory device on the net. Hidden in a route to the Asian matrix only accessible through the European array, Section 9 concludes that the device was hidden by Gouda. Unfortunately, Gouda has left no trace of his movements in the device. The Major prepares to dive into the device with Bouma and Ishikawa watching her closely. However, before she can dive, Aramaki notifies her that someone even more important than the external memory device has just surfaced...
In a new investigation to find a witness, Section 9 pursues the lead that few specialists could create Kuze's unique facial features. They finally locate the craftsman and rush to collect him, only to find that he has been murdered. Upon reviewing the security tapes to find his killer, they discover that the murderer resembles one of their own.
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 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.
The Tachikomas decide to skip a scheduled maintenance exam and investigate the Individual Eleven on their own. Batou learns about this and can't help but feel uneasy about it. Meanwhile, a Professor Asuda turns up missing after an explosion at the A.I. lab. While investigating the explosion, the Tachikomas experience an odd feeling of déjà vu; this, in spite of the fact that they had no prior memories of Asuda.
Ishikawa returns from the Peninsula with the latest intel on Kuze, but is surprised to learn of a possible refugee uprising. The Major and Aramaki are sent to see the Prime Minister to discuss this matter. While they wait, the rest of the team listens to Ishikawa's report on Kuze's past.
Heading to Taiwan, the Major meets with the local security bureau to learn about Kuze's time there. Afterwards, she runs into a boy who is in trouble. Motoko saves him at the last second and the boy, ever greateful, tags along with her.
The Major and Batou are flown to Berlin in an effort to track down a terrorist called "Angels Wing". While there, Batou attracts the attention of a young girl in a wheelchair. The girl is waiting for the yearly visit from her father, but Batou's appearance piques her curiosity
The Dejima refugees declare their self-governing status despite close scrutiny by the authorities. Kuze is suspected to be the mastermind behind this new resistance, and Section 9 is sent to detain him. At the same time, the Cabinet Intelligence Service sends in their own cyber-unit to capture Kuze.
With the Major learning too late to save one of their own from a refugee ambush, a somewhat demoralised Section 9 heads to the northern Japanese island of Etorofu to learn Kuze's next move. Making their way into Etorofu as well is Gōda's colleagues in the Cabinet Intelligence Service.
With the Major not far behind, Batou orders Saitou after Coil and then jettisons from his Tachikoma, who is battling an Armed Suit, and goes after Kuze. Upon catching up with the refugee leader, Batou tries to take Kuze in with brute force. Unfortunately, Kuze's body is made to take such a beating.
The city of Fukuoka is evacuated when a live nuclear bomb is found. With the Dejima refugees targeted as the prime suspects, the government sends the Self-Defence Forces into the city. Aramaki suspects the Cabinet Intelligence Service's involvement in this latest incident is deeper then it appears. Batou is sent to gather more information from Gōda.
With the recent events allegedly incited by the refugees, the government is left with no choice to declare martial law in Dejima. As the troops move in and the refugees fortify their position, Section 9 once again is forced into playing a role in order to keep their unit alive.
With the felling of Dejima Bridge by the refugees, a rumor circulates around the Cabinet that the refugees plan a mass suicide bombing using nuclear bombs. Unbeknownst to the populace, Prime Minister Kayabuki has been secretly arrested and taken to an unknown location. Aramaki, Togusa and Proto, in trying to help the P.M. are also taken into custody and secured nearby. At the same time, the rest of Section 9 enter Dejima and are promptly cut off from any outside help.
Having just attacked and destroyed the plane that had been jamming communication over Dejima, Kuze and some refugees come under fire from the Jigabachi helicopters. Seeing this, the Major moves closer to apprehending Kuze. Meanwhile, the Rangers of Section 4 begin their hunt for Batou, Bouma, Saitou, and Pazu, who are carrying one half of the plutonium.
Kuze and the Major gain an understanding of each other and agree to collaborate. Out in the ruins of Dejima, Batou continues his search for the Major. Aramaki is desperately using every political maneuver he knows to stop the conflict. Despite his efforts, a tactical nuclear warhead is launched and heads towards Dejima.
Much time has past since the end of the refugee issue and Section 9 has changed with it. Now a larger force, Section 9's only handicap is it is without the skills of Major Motoko Kusanagi, who left over two years ago. Togusa is now in charge of the section that will be put to the test when a mysterious entity dubbed the Puppeteer emerges and begins killing off members of a disenfranchised group of ex-military.