Stand Alone Complex takes place in the year 2030, in the fictional Japanese city of New Port. The story follows the members of Public Security Section 9, a special-operations task-force made up of former military officers and police detectives. The manga presents individual cases that Section 9 investigates, along with an ongoing, more serious investigation into the serial killer and hacker known only as "The Laughing Man."

Since being formed as a shadow peacekeeping organization, Section 9 has faced almost countless adversaries both in the real world and in cyberspace, but none like "The Awakened," a group of terrorists who seem to have the ability to take over the minds and bodies of almost anyone and use them to commit crimes against the state, leaving their pawns unaware of who was controlling them. When Major Motoko Kusanagi is able to capture one of the boys used as a pawn she hacks into his cyberbrain to find out who the ringleader is, but what she discovers will take her and the operatives of Section 9 on a journey deep into the heart of cyberspace, and the answers she finds will shake Section 9 to its core.

2030 Tokyo: While patrolling Tokyo's post-World War III refugee zones Togusa, the newest member of Section 9, discovers that one of the most powerful cyber-criminals his squad has ever faced has plans to kill their leader, Section 9 Chief Daisuke Aramaki, in one of three stories in this collection, and it will take all of the members of Section 9 to stop him. The action heats up in the stories "Double Targets," "First Love, Last Love" and "Revenge of the Cold Machines."

The year is 2030. Advances in robotics and cyberbrain technology have transformed the world into a miraculous place where almost anything is possible - even the melding of humans and machines. In this not-too-distant future, the crimes of flesh and metal are investigated by Section 9, an elite counterterrorist squad headed by Chief Aramaki and his cyborg sidekick, Major Motoko Kusanagi. When dead bodies, drained of blood and with two bite marks on their necks, start turning up on the streets of Tokyo, it isn't long before the entire city is in a panic. As Major Kusanagi and the other members of Section 9 investigate the killings they begin to wonder - is the killer a real vampire or something much worse? In a dark world of murder, where cyberbrain hacks and treacherous conspiracies reach to the furthest heights of government, Section 9 is all that stands between the people and anarchy.

This brand-new chapter fills in the gaps between The Ghost in the Shell: Human-Error Processor and Man-Machine Interface manga with a tense cyberpunk thriller written by Ghost in the Shell: Stand Alone Complex script writer Junichi Fujisaku. Just in time for the release of the new Ghost in the Shell: SAC_2045 anime on Netflix!

Hackers attempt to assassinate a politician during a speech preaching the advantages of cybernetic prosthetics. Fortunately, Togusa is there to whisk her to safety, and the investigation leads Batou to a suspicious factory in the artificial islands in southern Japan. Meanwhile, Chief Aramaki hears of a disturbing discovery at the other end of the country: dozens of artificial bodies, illegally dumped near a village where an anti-cyberization sect conducts their training and “rites.” Among the empty shells is one formerly inhabited by the woman who embodied Section 9 until she left it behind and disappeared: Major Motoko Kusanagi...

Togusa and Tsunagi are racing after a fleeing suspect when a van suddenly slams into the suspect's car, killing the van driver instantly. As Togusa hooks into the man's cyberbrain, he sees residual images of a group of children and a masked figure who says, “I am a warrior.” Later, an autopsy yields a shocking the driver was killed not by the collision, but by a neurotoxin derived from the venom of the African black mamba. Section 9 needs answers, so Togusa and Tsunagi get sent halfway across the world to the Sahel Special Economic Zone. What mysteries await them in the “oasis of the Sahara”?