Skull, the evil leader of the terrorist organization known as Black Ghost, has nine powerful cyborgs under his control. But Dr. Isaac Gilmore, the Black Ghosts cybernetics scientist, decides to go rogue, helping the cyborgs turn against Skull and his evil organization. Black Ghost wishes to start the next major world war by flooding the market with weapons of mass destruction. It seems the nine brave cyborgs have their work cut out for them, as Black Ghost is determined to bring those nine cyborgs down.

Cyborg 009: The Cyborg Soldier is a modern adaptation of the Cyborg 009 series that retells four of its primary story arcs. The first 48 episodes closely resemble the original series, whereas episodes 49-51 are an OVA exclusive, and are loosely based on the unfinished final chapter of the manga.