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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.

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 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.

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.

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.

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

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'.

As members of ESWAT, the elite forces serving Olympus, Deunan and Briaereos are deployed anywhere trouble strikes. Olympus finds itself under a stealth attack - cyborg terrorism, deadly nanotech zealots, and rioting citizens are just some of the threats that Deunan must contend with as she fights to save Olympus!

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 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 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?

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.

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

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.

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.

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.

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.

En un mundo compuesto por dos realidades, lo cotidiano y lo oculto tras ella, Thomas Anderson se ve obligado de nuevo a ir tras el conejo blanco. Dicha elección continúa siendo la vía de acceso a Matrix, que esta vez es más poderosa e intrincada que en ocasiones anteriores.

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.