A clandestine arms syndicate known as the Black Ghost organization abducts people from around the world, turning them into living weapons to fuel global conflicts for profit. Nine individuals from different nations, having been unwillingly transformed into cyborgs, reject their intended purpose. Led by the Japanese youth Joe Shimamura, designated Cyborg 009, they escape the organization alongside their creator, Dr. Gilmore, choosing to use their powers to fight against Black Ghost and protect world peace.

The team comprises a diverse cast, each with unique abilities. The leader is Joe Shimamura (009), who possesses an accelerator switch that allows him to move at superhuman speeds. Other members include Ivan Whisky (001), an infant with immense psychic powers like telepathy and telekinesis who requires extensive sleep to recover energy; Jet Link (002) from the United States, who has flight capabilities; and Françoise Arnoul (003) from France, who has enhanced hearing and vision for reconnaissance. The team also includes the German Albert Heinrich (004), whose extensive cybernetic modifications turn his body into an arsenal of weapons; the incredibly strong Native American Geronimo Jr. (005); the Chinese chef Chang Changku (006), who can breathe immense flames; the British shapeshifter Sir Great Britain (007); and the aquatic fighter from Africa known as 008 or Pyunma. Despite being created as the perfect soldiers, these cyborgs struggle with their lost humanity and often confront the trauma of their pasts, including false accusations of murder, lost loves, and the destruction of their former lives.

The central narrative follows their flight from Black Ghost, which deploys various agents and advanced weapons, such as robot dinosaurs and specially designed cyborg assassins like the electrical powerhouse Cyborg 0010. While hiding in Japan with Dr. Gilmore's colleague, the team faces constant threats from Black Ghost's forces, leading to a climactic confrontation that ends with the apparent destruction of the syndicate's base. The series explores notable arcs where characters confront their pasts, such as 007 encountering his ex-girlfriend's daughter and 004 remembering his fiancée who died trying to escape East Germany. After the final battle, the cyborgs attempt to live in peace, but their stories emphasize a recurring theme: the corruption that allows Black Ghost to exist lives in the human heart, suggesting their fight for justice may not be over.