While the New Generation Choujins are taking part in Fan Appreciation Day, The Cyborg arrives, takes Meat hostage, and challenges Mantarou to a fight inside Tokyo Tower.
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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 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.
009 Re:Cyborg follows a group of nine cyborgs, each of them created by a shadowy organization for use as weapons against humanity. The group turns on their creators to protect the population instead, using the powers given them to fight their creators.
In a utopian society created at the end of World War III, a female warrior who has been plucked from the badlands begins to see cracks in this new facade. And what does this community have planned for the rest of humankind?