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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.

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 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 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 year 2045, cybernetic mercenary Motoko Kusanagi returns to Section 9 to face a dangerous new threat: the posthumans.

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 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.

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.

The war on terror exploded, literally, the day Sarajevo was destroyed by a homemade nuclear device. The leading democracies transformed into total surveillance states, and the developing world has drowned under a wave of genocides. The mysterious American John Paul seems to be behind the collapse of the world system, and it's up to intelligence agent Clavis Shepherd to track John Paul across the wreckage of civilizations and to find the true heart of darkness—a genocidal organ.

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.

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?

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

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.

A member of an elite paramilitary counter-terrorism unit becomes traumatized after witnessing the suicide bombing of a young girl and is forced to undergo retraining. However, unbeknownst to him, he becomes a key player in a dispute between rival police divisions, as he finds himself increasingly involved with the sister of the girl he saw die.

Many years ago, a Great Civil War ravaged Japan, leaving the country fragmented between two regions: Kansai and Kanto. In Kansai, a group of six Akudama carry out missions given to them by a mysterious black cat, while evading the police. But a dangerous journey is about to unfold when a civilian girl becomes twisted into the Akudama's way of life and witnesses their criminal drives.

Set in a future world. Japan has created a great medical technology that controls ethics, health, and social interaction to create a perfect world. Three young girls attempt to stand up to this by committing suicide, but it doesn't work. Years later, Tuan, one of the girls who attempted suicide must prevent a crisis that threatens this "perfect" world.

On the planet Latimer, Takeshi Kovacs must protect a tattooist while investigating the death of a yakuza boss alongside a no-nonsense CTAC.

Ten years ago, a mysterious spatial anomaly now known as "Heaven's Gate" appeared in South America, shortly followed by the opening of "Hell's Gate" in Tokyo altering the sky and wreaking havoc on the landscape. The real stars disappeared, replaced by false stars. During this time, people possessing various special abilities — called "Contractors" — emerged, each capable of different supernatural feats. Following the disastrous Heaven's War, the United States lost its dominant position as a superpower to a mysterious organization named the Syndicate. The story revolves around a Chinese contractor codenamed "Hei" as he undertakes various espionage and assassination missions in Tokyo.

The story revolves around Shu Ouma, a high school boy who inadvertently obtains an ability called "The Power of the Kings" that enables him to draw out items called "Voids" from other people. He is then thrown into the conflict between a resistance group called Funeral Parlor which aims to restore Japan's independence from a quasi-governmental organization known as the GHQ. In the process, Shu has to deal with the burden his ability puts on his shoulders and the horrific mystery of his past.