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. So He gave unto man an opportunity to atone for his misdeeds and flame and smoke and the roar of a lion descended upon earth and shattered the many towers to dust.The first arc was serialized in Weekly Shōnen King ( Shōnen Gahosha).

Scattering across the land and laying it to waste, man turned a deaf ear to His Voice. But those who dwelt upon the land, through vanity, cunning and greed, attempted to build a multitude of towers whose tops reached unto heaven, and accumulated great wealth on earth. 'In the beginning was the Voice, and the word was Him and all obeyed His word in great awe. So He gave unto man an opportunity to atone for his misdeeds and flame and smoke and the roar of a lion descended upon earth and shattered the many towers to dust.'

Decades later, the nine cyborgs seem to be untouched by time, but they live in a world where 'justice' has as many nuances as the number of people living on the planet. The nine cyborgs rebel and start to fight against their creators in the name of justice and world peace. Nine regular humans from different parts of the world are abducted and transformed into cyborgs with astounding powers for the purpose of being used as weapons.

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