A long arc consisting of many short arcs, this series dealt with the battle against Neo Black Ghost as well as the emotional trauma of the 00 Number Cyborgs.

The seventh arc was serialized in Weekly Shōnen Sunday ( Shogakukan) alongside the revival anime. Arcs such as the Deinonychus Arc (appeared in Monthly Shōnen Jump ( Shueisha)) and Green Hole Arc (appeared in Play Comic ( Akita Shoten)) were depicted, then long after, the Underwater Pyramid Arc was serialized in Monthly Manga Shōnen ( Asahi Sonorama). The sixth arc followed closely after the fifth arc.

The story deals with legendary and mythical like characters challenging the 00 Number Cyborgs. The fifth arc was serialized in Shōjo Comic ( Shogakukan), and included the Wind City Arc, the Snow Carnival Arc, and the Edda Arc. Ishinomori would not resume the series for a few years after this. Ishinomori resumed and retold the interrupted Angels Arc with a new plot, but the series once again ended abruptly. The fourth arc, called The Battle of the Gods Arc, was serialized in COM ( Mushi Production). The series abruptly ended during the Angels Arc. The third arc, serialized in Bōken Ō ( Akita Shoten), contained 6 story arcs, including the Monster Island Arc, the Middle East Arc, and the Angels Arc. As such, 001 was able to use his telekinetic powers at the last minute to retrieve 002 and 009 from their plummet before death. In the final scene, 009 and 002 fall into Earth's atmosphere and are seen as a shooting star by two small children, one of whom wishes for a toy gun and the other for world peace (a scene reminiscent of Ray Bradbury's Kaleidoscope). The story ends with the final battle against Black Ghost. The story is highly influenced by Edgar Rice Burroughs' Earth's Core series, including an expedition to the center of the Earth with a drill tank and a reptile race who can use telepathy and grow wings.

The second arc, called The Underground Empire Yomi Arc, appeared in Weekly Shōnen Magazine ( Kodansha) alongside the release of the film version. It ended with the battle against the Mythos Cyborgs. It depicts Cyborg 009's origin story, the escape from Black Ghost, and the group running from the cyborg assassins. The first arc was serialized in Weekly Shōnen King ( Shōnen Gahosha).

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