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The story follows Motoko Kusanagi, a highly skilled member of the military, whom upon meeting Daisuke Aramaki, a current chief of the Public Security Section 9, in less than desirable conditions struggles to clear her name whilst forming her own independent team with the highest priority under the sponsorship and guidance of the chief Aramaki himself.

Humanity has found a way to achieve infinite energy by using coils to draw it from the fourth plane: dimension "W". With the production of coils having been monopolized by the New Tesla energy company, freelance collectors are hired to find and remove any illegal, unofficial coils. This is the story of collector Kyōma, who also happens to have a huge hatred towards coils. During one of his missions he stumbles upon a female android that perceives herself as being human, leading the two to enter an unlikely partnership.

Cosmic Era 71. Mankind has developed into two subspecies: Naturals, who reside on Earth, and Coordinators, genetically enhanced humans capable of withstanding the rigors of space who inhabit orbital colonies known as PLANTs. The story revolves around a young Coordinator named Kira Yamato, who becomes involved in the war between the two races after a neutral space colony secretly developing mobile suits for the Earth Alliance is attacked by the PLANTs' military force, ZAFT.

The year is 2307 A.D. Although fossil fuels have been depleted, humanity has obtained a new source of energy to replace them, in the form of a large-scale solar power generation system based on three huge orbital elevators. However, the benefits of this system are available only to a handful of major powers and their allies. In this world of never-ending conflict, a private armed organization appears, dedicated to the elimination of war through armed force. Its name is Celestial Being, and it is in possession of "Gundam" mobile suits.

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.

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 year 2024, the world has collapsed. Grotesque monsters lurk amongst the ruins of Japan, while remaining people scrape together what they can to survive. Kiruko, an odd-job girl in Nakano, accepts a mysterious woman's dying wish to take a boy named Maru to a place called Heaven. Maru is convinced that there will be a boy there who looks exactly like him.

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.

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

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