The year is 2013. Skyscraper bombings are happening all over the world, by the direction of a force called "His Voice". 27 years after the 00 Cyborg team disbanded, 007 now works for ISIS and 002 now works for NASA after a falling out with the team and Joe. The two agents meet at a bar in New York City to exchange intel about "His Voice" and Pyunma's findings of a fossil which resembles an angel's skeleton possibly being related to it. The intelligence agencies of the world are all whispering about the incidents being related to His Voice, the unknown entity that is controlling operatives of the bombings.
Joe Shimamura, who had his memories blocked and reset every 3 years by Professor Gilmore, is now a typical high school student, falsely believing that he has an unseen family and friends due to the "Augmented Reality" implanted in his brain. He also has a girlfriend named Tomoe, who seems familiar to him in some way. However, Joe is hearing His Voice due to his cybernetic brain. We learn that he was about to plant a bomb at the Roppongi Hills Tower, until 005 and 003 came to reactivate his memories. Dr. Isaac Gilmore suspects that these were orchestrated by the United States government's National Security Agency, in a bid to regain dominance as a global superpower.
In Dubai, a B-2 bomber flown by an US Air Force pilot under the control of His Voice launches missiles at the city, with 002 in pursuit to intercept. 009 appears and uses his Acceleration mode to destroy the missiles. After 009 gets knocked off the plane by 002 in a fight, the pilot fires a nuclear bomb which destroys the entire city and kills the population of Dubai. 009 uses his Acceleration Mode to outrun the blast, but is left unconscious and lying on the beach. In his mind, he pictures himself in the burned out city, despondent over his failure. Tomoe appears to comfort him, and remind him of his purpose. Due to the EMP effects of the nuclear blast, communications are down and the team thinks Joe is dead.
Nuclear missiles are fired and 003 fires interceptors and disables all of them except for one. With no time to lose, Joe requests 001 to teleport him into space to disarm the missile. 001 agrees but states he will be unable to return him to Earth at that distance, as Ivan would exhaust his power doing so.
002 flies up to try to help 009 but ends up burning out his rockets and damaging his stabilizers, causing him to plummet towards Earth. Joe then speaks to God and says that while humanity is foolish and causes suffering towards each other, he believes in them because they have such great potential to go beyond those vices and make their dreams become reality. He then pleads to him that the earth be spared, only for the bomb to detonate in space with Joe on top of it, the light of the explosion forming a cross. Francoise watches two falling stars, and silently prays upon both.
After some indeterminate point of time, Joe finds himself waking up in an apartment in a place that appears to be Venice, and sees Francoise walking across a canal. She explains that he's in her "safe house". Jet, Great Britain, and Pyunma also find themselves in the mysterious city, which Dr. Gilmore explains is the world created by His Voice. Back in the safe house, Joe and Fran talk about God for a bit and then the camera pans behind them to reveal that one of the angel skeletons is in her living room as a decoration.
The movie's final shot after the credits roll ends with the image of an angel skeleton on the surface of the Moon.009: Mamoru Miyano (Japanese), Jason Griffith (English)
008: Noriaki Sugiyama (Japanese), Marcus Griffin (English)
007: Hiroyuki Yoshino (Japanese), John White (English)
006: Tarou Masuoka (Japanese), Michael Sorich (English)
005: Teruyuki Tanzawa (Japanese), Patrick Seitz (English)
004: Toru Ohkawa (Japanese), Dave B. Mitchell (English)
003: Chiwa Saito (Japanese), Erin Fitzgerald (English)
002: Daisuke Ono (Japanese), Marc Diraison (English)
001: Sakiko Tamagawa (Japanese), Stephanie Sheh (English)
Professor Gilmore: Nobuyuki Katsube (Japanese), George C. Cole (English)
A 3DCG movie produced by Production I.G., Sanzigen and Ishimori Productions, was released on October 27, 2012. Kenji Kamiyama is the director and writer. Kenji Kawai, who has worked before with Kamiyama on Moribito: Guardian of the Spirit and Eden of the East, is composing the music. The film was released in Japan on October 27, 2012. It will also open simultaneously in more than five Asian regions, including Hong Kong, Taiwan, Singapore, Malaysia, and South Korea. A manga adaptation by Gatou Asou, character designer for Moribito and Occult Academy, is currently being serialized in Square Enix's Monthly Big Gangan. The UK anime distributor Anime Limited has announced that they have acquired the movie and will produce an English dub at NYAV Post. Madman Entertainment also has rights to release the film in Australia and New Zealand. At Anime Expo 2013, Funimation had announced that they acquired the film for North America.