The story was based on the original
Ghost in the Shell manga chapter,
Robot Rondo, albeit heavily modified from the original story. The story begins in the year 2032.
Batou, originally partnered with Major Kusanagi, who disappeared at the end of the first film is now teamed with Togusa.
Public Security Section 9 investigates 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"
that was created by using an illegal method using a "ghost-dubbing"
machine that produces "information-degraded, high-volume copies", but
killing the original in the process. 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.
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 she'll always be with him right before
the gynoid deactivates. Yet, victorious Batou, when confronted with one
of the girls he saved, doesn't share her joy and sternly remarks that
she and Volkerson had no regard for "innocent" dolls they doomed to have
personalities ("ghosts"), kill people and finally die from the hands of
the law.
