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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 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 a dystopia riddled with corruption and cybernetic implants, a talented but reckless street kid strives to become a mercenary outlaw — an edgerunner.

On a terraformed post-disaster Mars, a group of child security agents rebel against the adults who betrayed them and the oppressive Earth government.