In late 1997, the original manga creator Shotaro Ishinomori is visited by Cyborg 001, who appears from within one of his drawings. The cyborg reveals that he and his eight comrades are real individuals living in the year 2012, and that Ishinomori's manga was inspired by telepathic visions sent back in time. Dr. Gilmore also travels from the future to explain that a world-ending catastrophe is approaching. The creator learns that his two previous attempts to end the series, the Angel arc and the Battle with the Gods arc, were based on real events that the cyborgs experienced, but neither provided a true conclusion. With his own health failing, Ishinomori resolves to write a final chapter titled 2012 009 Conclusion: GOD'S WAR, hoping to give his characters the happy ending they need to survive.

The story then shifts to the year 2012. The nine cyborgs have scattered across the globe, attempting to live normal lives after their battles against the Black Ghost organization. Joe Shimamura, designated Cyborg 009, is the team's leader. His comrades include the psychic infant Ivan Whisky or 001, the impulsive American Jet Link or 002, the sensitive French dancer Francoise Arnoul or 003, the stoic German marksman Albert Heinrich or 004, the powerful Brazilian Geronimo Jr. or 005, the Chinese cook and philosopher Chang Changku or 006, the shape-shifting British actor Great Britain or 007, and the aquatic Norwegian fisherman Pyunma or 008.

The peace is broken when each cyborg is individually drawn into a series of supernatural and disturbing events. Jet Link, now working as a private detective in New York City, investigates a missing persons case that leads him to a black magic cult called the Fucho Cult. The cult is aided by former Black Ghost scientists who have created a monstrous entity known as the God of Gods, which turns on its masters and disappears. Francoise is approached in Paris by a mysterious archaeologist who gives her an ancient crystal containing the eye of a statue. She soon finds herself hunted by angelic beings who claim that humanity was a mistake and that the year 2012 is the time of their harvest. Each of the other cyborgs encounters similar inexplicable threats across the world, from the deep sea to the Amazon rainforest, all connected to entities that claim to be gods.

The separate narratives converge as the cyborgs learn that the entities they are facing are not aliens or advanced weapons, but something far older. These beings, which humanity has worshipped as angels and deities throughout history, have decided to erase their creation. The cyborgs are identified as a unique threat because their mechanical bodies and human spirits exist outside the natural order. As the entities prepare to unleash a final catastrophe on Tokyo, the team reunites at Dr. Gilmore's manor. They must unlock new psychic powers, including teleportation and molecular manipulation, to stand against forces that view them as abominations.

The final battle takes place during a massive earthquake that destroys the Japanese capital. The cyborgs face the full power of the divine entities, suffering severe injuries and making immense sacrifices. The story builds toward a confrontation that questions the nature of humanity and divinity. The conclusion deviates from standard action story resolutions, offering an ambiguous ending that transcends traditional science fiction and leaves the ultimate fate of the world and the cyborgs open to interpretation, fulfilling the dying wish of the original creator to find a final image for his lifes work.