Watch Ghost In The Shell: Stand Alone Complex

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.

As the bombing of Dejima escalates, the Major catches up with Kuze. She explains the whole situation to him, and he agrees to follow her. The are about to leave when both are attacked by the Self-Defense forces and in the confusion are trapped under the rubble. Meanwhile, Togusa rescues the Prime Minister and brings her back to her office. There, Aramaki hopes her influence will stop the launching of the ultimate weapon. Back out in Dejima, Batou reasons with Section 4.

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. Fearing this, the Cabinet steps up the attack against the city. Unbeknownst to them, 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 in her office. With Section 9 having entered the non-communication zone and Aramaki being cut off from communication, Ishikawa and a Tachikoma make their way to SPRING-8 on their own. Meanwhile, Gouda has sent an unwitting Section 4 after Section 9 to retrieve the plutonium.

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.

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 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.

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.

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.

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

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.

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.

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.

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.

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.

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...

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.

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.

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.

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.

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...

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.

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.

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...

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.

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.

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.