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.

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 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'.

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.

The year is 2030, and an influx of refuges have effortlessly transformed themselves into a terrorist organization known as the "Individual Eleven." With a sadistic intent of mass destruction, will they triumph in victory or discover the gloomy pitfalls of defeat?

In the year 2045, after an economic disaster known as the Synchronized Global Default, rapid developments in AI propelled the world to enter a state of "Sustainable War". However, the public is not aware of the threat that AI has towards the human race. A compilation film with newly added footage.

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 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.

2112; the summer before Akane Tsunemori was assigned to Division One of the Public Safety Bureau's Criminal Investigation Department. Teppei Sugo, an accomplished pilot of the Defense Army's 15th Integrated Task Force, joins the military operation in Okinawa. Three months later, an unmanned combat drone opens fire on the Ministry of Defense in Tokyo. Enforcer Tomomi Masaoka of CID Division One is dispatched to Sugo's military base to investigate the truth behind this case.

Following the incident in the Southeast Asia Union in 2116, Shinya Kogami resumes his vagrant journey. In a small South Asian nation, Kogami rescues a bus of refugees under attack by armed guerrilla forces. Among the refugees is a young lady by the name of Tenzin, who begs Kogami to teach her how to retaliate against the enemy. Just what does the girl who wishes for revenge and the man who has exacted revenge see as they gaze upon the edge of a world from which there is no escape?

The year is 2030 and six years have passed since a criminal known only as "The Laughing Man" swept through top medical nanotechnology firms committing acts of cyber-terrorism, kidnapping, and espionage leaving no known suspects. New information is revealed, as Section 9 enters the hunt for a suspect capable of unfathomable actions in this compilation of Stand Alone Complex content.

Cyborg detective Batou is assigned to investigate a series of murders committed by gynoids—doll-like cyborgs, which all malfunctioned, killed, then self-destructed afterwards. The brains of the gynoids initialize in order to protect their manufacturer's software, but in one gynoid, which Batou himself neutralized, one file remains: a voice speaking the phrase "Help me."

In his travels as a bounty hunter, Hunter–Warrior and cyborg healer Ido one day discovers and repairs the remnants of a cyborg whom he names Gally. Though possessing the body of a young woman, Gally now embodies Ido's most sophisticated and lethal cybernetic skills. The preternaturally strong, amnesiac Gally begins to forge a life for herself in a world where every day is a struggle for survival.

In a universe where the Cold War never ended and growing conflicts result in the rapid advancement of technological warfare, the cyborg spy Mylene Hoffman of the 00 Organization battles the agents of the Eastern block in a game of high tech espionage.

Rescued by Doctor Easter from a deadly assault on their headquarters by Dimsdale Boiled, Rune Balot finds temporary shelter in "Paradise," a high-tech laboratory where the Scramble 09 protocol originated. While the severely injured Oeufcoque regenerates in a healing vat, Rune struggles to find the answers within herself that will let her equally injured psyche find some measure of peace. But as the search for clues to the location of Shell's hidden memories continues, Boiled finds them again, and Rune and the Doctor decide it's time to carry the war to the enemy.

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

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.

The Batman family has returned to the present to discover that Japan has disappeared, and a giant island - Hinomoto - is now in the sky over Gotham City. At the top sit the Yakuza, a group of superpowered individuals who reign without honor or humanity and look suspiciously like the Justice League. Now, it’s up to Batman and his allies to save Gotham!

Fourteen years after Third Impact, Shinji Ikari awakens to a world he does not remember. He hasn't aged. Much of Earth is laid in ruins, NERV has been dismantled, and people who he once protected have turned against him. Befriending the enigmatic Kaworu Nagisa, Shinji continues the fight against the angels and realizes the fighting is far from over, even when it could be against his former allies. The characters' struggles continue amidst the battles against the angels and each other, spiraling down to what could inevitably be the end of the world.