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After 250 years on ice, a prisoner returns to life in a new body with one chance to win his freedom: by solving a mind-bending murder.

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.

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.

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 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?

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

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.

A large scale catastrophe is occurring across the planet. Ability users are discovered after the appearance of a mysterious fog, apparently having committed suicide, so the Armed Detective Agency sets out to investigate these mysterious deaths. The case seems to involve an unknown ability user referred to as "Collector," a man who could be the mastermind behind the incident. Trust and courage are put to the test in order to save the city of Yokohama and ability users across the world from the grip of Collector where the Armed Detective Agency forms an unlikely partnership with the dangerous Port Mafia.

A new member from the Black Organization that shrunk Shinichi's body manages to find out about Shinichi's transformation into Conan. This discovery starts to put those around him in danger as Gin and the other Black Organization members start to take action.

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.

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.

In February 1999, a string of murders has Shiki Ryougi and Mikiya Kokutou on edge. These crimes share a disturbing resemblance to a similar set of homicides from 1995, when Shiki and Mikiya first met, and awaken a dark, murderous desire that has laid dormant within Shiki's soul ever since then.

Rising pop star Mima Kirigoe quits singing to pursue a career as an actress. After she takes up a role on a popular detective show, her handlers and collaborators begin turning up murdered. Harboring feelings of guilt and haunted by visions of her former self, Mima's reality and fantasy meld into a frenzied paranoia.

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.

Tomoe Enjou is attacked by bullies from his old school and saved by Shiki Ryougi. He asks her to hide him at her place and admits that he killed someone. Several days later, there are still no broadcasts about the murder as if it didn't happen... and when the victims are found, they're alive and unharmed.

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.