The story is loosely based on Ghost in the Shell manga chapter "Robot Rondo" (with elements of "Phantom Fund").

Since the gynoids all malfunctioned without clear cause, the deaths are believed to be premeditated murders; Batou and Togusa are sent to investigate possible terrorist or political motives.

Section 9 concludes human sentience is being artificially duplicated onto the dolls illegally, making the robots more lifelike, and possibly acting as a motive in the murders.

Called to a homicide scene, information warfare/technology specialist Ishikawa explains the victim is Jack Walkson, a consignment officer at gynoid company LOCUS SOLUS, who may have been killed by the yakuza.

While having his damaged arm replaced, Batou is informed by Ishikawa that his e-brain was hacked, causing him to shoot himself and attack the store occupants.

Ishikawa explains that Batou was hacked in order to cause further scandal following his yakuza assault in an attempt to stop the Section 9 investigation.

Seemingly dead, Kim soon reveals he "lives" inside the shell of a human-sized marionette, and discusses philosophy with his visitors.

Warned again by the Major, Batou realizes that Kim has secretly hacked into his and Togusa's e-brains, and is currently trapping them in a false reality.

Resolved to gather material evidence, Batou infiltrates the LOCUS SOLUS headquarters ship while Togusa remotely hacks its security systems using an unaware Kim as a proxy.

Simultaneously, a hidden virus loads a combat program into the production-line gynoids, causing them to attack everyone aboard, easily slaughtering the poorly armed and panicked security force.

Hiring the yakuza to traffic young girls, LOCUS SOLUS duplicated their consciousnesses into the gynoids, giving them human "ghosts" to make them more realistic.

This caused the gynoids to murder their owners, allowing Walkson to attract police attention and indirectly kill the yakuza boss.

Despite Walkson's actions saving the girls, Batou objects that he also victimized the gynoids as well, causing them severe distress by giving them damaged ghosts.

Other numerous quotations in the film come from Buddha, Confucius, Descartes, the Old Testament, Meiji-era critic Saitō Ryokuu, Richard Dawkins, Max Weber, Jacob Grimm, Plato, John Milton, 14th-century playwright Zeami Motokiyo, the Tridentine Mass, and Julien Offray de La Mettrie, French Enlightenment philosopher and author of "Man a Machine".

The company LOCUS SOLUS is named for the 1914 novel by Raymond Roussel, which also shares certain thematic elements with the film, such as a mansion containing tableaux vivants.

I attacked Innocence as a technical challenge; I wanted to go beyond typical animation limits, answer personal questions and at the same time appeal to filmgoers.

[6] He credited Jean-Luc Godard for the idea of including quotes by other authors: "[The texts] ... give a certain richness to cinema because the visual is not all there is.

Only doing 3D does not interest me.On the overall message of the film, the director said "This movie ... concludes that all forms of life – humans, animals and robots – are equal.

Some fans saw this as conflicting with Oshii's statements that the film wasn't, in actuality, a standard Hollywood-esque sequel, and was able to, and intended to, stand on its own.

Bandai Entertainment under license from Paramount and DreamWorks created a second dub for the North American market using most of the voice actors from the Manga/Madman version making some changes to the cast and production team and using Animaze's studio.

[9] As he expressed in the liner notes, he agreed with Mamoru Oshii that the soundtrack pattern itself somewhat after and "would follow the music from the original film."

Additionally, Oshii made specific requests for "a huge music box," a "jazzy theme," and a "reprise of the song 'Follow Me'".

The minyoh singers chorus, heard in the "Chants" in the first movie, and in the "Ballade of Puppets" in Innocence, was expanded to include 75 performers, which proved challenging to record.

The consensus states: "The animation is lovely, but the plot is complex to the point of inscrutability, leaving Ghost in the Shell 2: Innocence both original and numbing.

[15] The film was praised by Manohla Dargis of the New York Times, who wrote "Innocence doesn't just reveal a wealth of visual enchantments; it restates the case that there can and should be more to feature-length animations than cheap jokes, pathos and pandering.

"[16] In contrast, criticism rests upon a number of factors, often cited to be overly heavy on philosophical dialogue and thus hard to follow,[17] and its ending has been described as weak and unmeaningful in the arc of character development.

On the same day, Bandai Namco Arts and Disney teamed up to release an Ultra HD Blu-Ray combo pack containing both movies for a limited time.

Bandai Entertainment has released the film on Blu-ray and DVD in the US, with an English dub also featuring the cast used in Ghost in the Shell: Stand Alone Complex.