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In the future when technological enhancements and robotics are a way of life, Major Motoko Kusanagi and Section 9 take care of the jobs that are too difficult for the police. Section 9 employs hackers, sharpshooters, detectives and cyborgs all in an effort to thwart cyber criminals and their plans to attack the innocent.

In the year 2029, the barriers of our world have been broken down by the net and by cybernetics, but this brings new vulnerability to humans in the form of brain-hacking. When a highly-wanted hacker known as 'The Puppetmaster' begins involving them in politics, Section 9, a group of cybernetically enhanced cops, are called in to investigate and stop the Puppetmaster.

The story takes place in the year 2034, two years after the events in Ghost in the Shell: S.A.C. 2nd GIG. Female cyborg Major Motoko Kusanagi has left Public Security Section 9, an elite counter-terrorist and anti-crime unit specializing in cyber-warfare, which has expanded to a team of 20 field operatives with Togusa acting as the field lead.

The upcoming installment's story takes place amidst signs of postwar reconstruction in the winter of 2028. Tensions are rising in New Port City as demonstrations are held concerning the interests of foreign cartels. This leads to a shooting incident involving riot police. It all started with a cyberbrain infection released by the terrorist "Fire Starter." An independent offensive unit led by Makoto Kusanagi entrusts the suppression of the situation to their ghosts and aims for their own justice. Below the surface of the incident, lies the "tin girl" Emma and the "scarecrow man" Burinda Junior. As Kusanagi deals with the incident, she draws near to what those two ghosts were seeking.

The story is set in 2027, one year after the end of the fourth non-nuclear war. New Port City is still reeling from the war's aftermath when it suffers a bombing caused by a self-propelled mine. Then, a military member implicated in arms-dealing bribes is gunned down. During the investigation, Public Security Section's Daisuke Aramaki encounters Motoko Kusanagi, the cyborg, wizard-level hacker assigned to the military's 501st Secret Unit. Batou, a man with the "eye that does not sleep," suspects that Kusanagi is the one behind the bombing. The Niihama Prefectural Police detective Togusa is pursuing his own dual cases of the shooting death and a prostitute's murder. Motoko herself is being watched by the 501st Secret Unit's head Kurutsu and cyborg agents.

Freed of her responsibilities with the 501 Organization, Motoko Kusanagi must now learn how to take orders from Aramaki. Someone hacks the Logicomas, and Batou enlists the help of former army intelligence officer Ishikawa and former air artillery expert Borma. Kusanagi also seeks to enlist ace sniper Saito and undercover cop Paz into the new Public Security Section 9.

In the year 2113, people are given brain scans to determine how likely they are to commit a crime. Those who fail are apprehended, or even killed.

In the year 2029, Section 9, a group of cybernetically enhanced cops, are called in to investigate and stop a highly-wanted hacker known as 'The Puppetmaster'.

Inspector Kei Mikhail Ignatov finds himself involved with an organization named Bifrost with the possibility of freeing his wife if he betrays Unit One. Koichi Azusawa coordinates an assault on the Public Safety Bureau tower using his hacker Obata, locking down the building and kidnapping Inspector Arata Shindo. Azusawa demands that governor Karina Komiya resign from her position.

In a futuristic Japan, the Sibyl System is charged with keeping the peace. When the state of SEAUn brings the Sibyl System in to test its effectiveness, it becomes a haven of peace and safety—for a time. Eventually, terrorists from SEAUn begin appearing in Japan, somehow slipping through the System's security and attacking from within. Desperate for answers, Inspector Akane Tsunemori is sent overseas to bring the terrorists to justice. But when her investigation forces her into a standoff with an old ally, will she be able to pull the trigger?

In a utopian society created at the end of World War III, a female warrior who has been plucked from the badlands begins to see cracks in this new facade. And what does this community have planned for the rest of humankind?

In the winter of 2117, a runaway vehicle crashes into the Public Safety Bureau Building. The driver is identified as Izumi Yasaka, a psychological counselor at the Sanctuary, a Latent Criminal Isolation Facility in Aomori Prefecture. But right before her interrogation, Inspector Mika Shimotsuki and Enforcer Nobuchika Ginoza are tasked with promptly escorting Yasaka back to Aomori. What awaits them there is a False Paradise.

In the midst of societal conflict in the futuristic city of Metropolis, Kenichi and his uncle Shunsaku Ban set out to uncover the mystery behind the first human-like robot, Tima.

Tras esquivar la muerte, Major Kusanagi resucita como cíborg y encabeza un equipo de caza de ciberterroristas. Pero un pirata informático se reserva otros planes.

Thousands of years after Earth’s atmosphere was destroyed, adventure blooms in the strangest of places. The domed city of Romdo is supposed to be perfect, but Re-l Mayer, a young female inspector from the Civilian Intelligence Office, knows better. In this place where humans and robots coexist, she receives a strange message: something is awakening!

A mysterious suicide and a series of unmanned robot run-aways sparks off a Police investigation into the suspicious software on-board thousands of industrial robots around Tokyo.

A Japanese police unit who use giant anthropomorphic robots (called Labors) is caught up in a political struggle between the civilian authorities and the military when a terrorist act is blamed on an Air Force jet. With the aid of a government agent, the team gets close to a terrorist leader to stop things from going out of control when after the military is impelled to impose martial law.

Rune Ballot is a down-and-out teen prostitute in Mardock City. One day, she's picked up by an ambitious casino manager named Shell who gives her everything she could want. Renewed by a false innocence, a false past, and now the false life Shell has given her, Ballot feels grateful. However, she can't help but be curious about why he's done so much for her, so she does some research about his past on a computer. This turns out to be a mistake which will change her life greatly. When Shell finds out what she's done, he attempts to burn her to death by blowing up her car.

The year is 2048. By mandate, every cop must partner with a robot. Detective John Kennex returns to work after waking up from a 17-month coma. As he adjusts to working with his new partner, Dorian, a discontinued android with unexpected emotional responses, John also must learn to get along with his new colleagues.

In the distant technological future, civilization has reached its ultimate Net-based form. An "infection" in the past caused the automated systems to spiral out of order, resulting in a multi-leveled city structure that replicates itself infinitely in all directions. Now humanity has lost access to the city's controls, and is hunted down and purged by the defense system known as the Safeguard. In a tiny corner of the city, a little enclave known as the Electro-Fishers is facing eventual extinction, trapped between the threat of the Safeguard and dwindling food supplies. A girl named Zuru goes on a journey to find food for her village, only to inadvertently cause doom when an observation tower senses her and summons a Safeguard pack to eliminate the threat. With her companions dead and all escape routes blocked, the only thing that can save her now is the sudden arrival of Killy the Wanderer, on his quest for the Net Terminal Genes, the key to restoring order to the world.