Much of the storyline is taken from the original Ghost in the Shell manga, from a chapter called Robot Rondo, albeit heavily modified from the original tale. The story of Innocence begins in 2032, when cities are inhabited by the dwindling races of humans, purely mechanical androids, and cyborgs like Batou who still have a ghost (the in-universe term for the human spirit), but are vulnerable to ghost hacking.

The movie features several characters from the preceding movie, like Togusa, the most organic member of the team, Chief Aramaki and Batou, as the protagonists. Batou was originally partnered with Major Kusanagi, who disappeared at the end of the first film. He's now teamed with a reluctant Togusa, who says he never asked for the assignment and that he knows he could never compare to the Major.

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