In the year 2074, the cybernetics market is dominated by two rival companies: USA's Pinwheel Robotics and Japan's Kobayashi Electronics. Cyborgs are commonplace, used for anything from soldiers to prostitutes. Casella Reese is a prototype cyborg developed for corporate espionage and assassination. She is filled with a liquid explosive called Glass Shadow. Pinwheel plans to eliminate the entire Kobayashi board of directors by using Casella

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 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.

A lonely university student develops a romance with a beautiful interesting woman, who turns out to be a cyborg from the future.

A small band of resistance fighters battle the cyborgs that have taken control of the planet.

When space galleon cabin boy Jim Hawkins discovers a map to an intergalactic "loot of a thousand worlds," a cyborg cook named John Silver teaches him to battle supernovas and space storms on their journey to find treasure.

When the evil Dr. Hell attacks the Earth, the mighty giant mecha Mazinger Z is formed to stop him.

Mark 13 is a government-built killing machine programmed with artificial intelligence, able to repair and recharge itself from any energy source. Through a series of coincidences, the cyborg's head ends up in the home of a sculptress as a bizarre Christmas present from her boyfriend. Once inside its new home, the cyborg promptly reconstructs the rest of its body using a variety of household utensils and proceeds to go on a murderous rampage.

The time is in the future and the youth gang violence is so high that the areas around some schools have become "free-fire zones", into which not even the police will venture. When Miles Langford, the head of Kennedy High School, decides to take his school back from the gangs, robotics specialist Dr. Robert Forrest provides "tactical education units". These are amazingly human-like androids that have been programmed to teach and are supplied with devastatingly effective solutions to discipline problems. So when the violent, out-of-control students of Kennedy High report for class tomorrow, they're going to get a real education... in staying alive!

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.

After a nuclear war society breaks down into two groups, the evil Euraks, and the rebel Federation. A mercenary named Parsifal is hired by the Federation to infiltrate New York City, which is controlled by the Euraks, to rescue the only fertile woman left on Earth.

In the future, chaos is rampant as 'information terrorists' threaten to destroy order in society. Alex is a part-man, part-machine LAPD cop who is the best at what he does. When one of the terrorists calls him a machine, Alex questions his humanity and decides to leave the force. His final assignment is to apprehend an old colleague who has stolen some data. However, there is more than meets the eye and Alex must question his allegiance.