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Story

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.

The special officers of Public Security Section 9 are investigating a cyborg corporation called LOCUS SOLUS (from the novel of the same name by French author Raymond Roussel) and its gynoids—androids made in the form of young women and used as sex dolls—that have killed eight people, having deliberately been tampered with in order to trigger a police investigation. The dolls possessed a "ghost" (which made them so desirable) that was created by using a "ghost-dubbing" machine, an illegal procedure which produces "information-degraded, high-volume copies", but results in the death of the originals. Young girls were kidnapped by the Yakuza and sold to LOCUS SOLUS for this process. Two of the girls conspire with a LOCUS SOLUS shipping inspector named Volkerson to cause the malfunctions and thus draw official attention to their plight. Batou's body is fully artificial. As the movie's trailer dramatically posits, "the only remnants left of his humanity, encased inside a titanium skull shell, are traces of his brain, and the memories of a woman called Motoko Kusanagi." Major Motoko Kusanagi, the protagonist of Ghost in the Shell, is listed as missing, although government agents are still looking for her as she has confidential knowledge on Project 2501. In the film, Batou explains to Togusa that he helped the Major escape because the government only cared about what she knew and not her as a person.

In the climax of the film, when Batou is being overwhelmed by Locus Solus guards and gynoids killing each other, Kusanagi and Batou are reunited in the middle of a firefight when she downloads a part of her consciousness into an empty gynoid. After "Kusanagi" has fulfilled her task, she reassures Batou that "I'll always be with you online"; then the gynoid deactivates.

Source: Wikipedia