The storyline of the game takes various bits of the manga and mixes them together. It is a merger of "Assassins", "Mythos", and "The Underground Empire of Yomi".
The art style of the FMV cutscenes mostly references the character designs as seen from the film Cyborg 009 The Movie: Legend of the Super Galaxy (save for 001 having white hair from the manga), with the voice cast from the film reprising key roles. However, the soundtrack in the game is sourced from the 1960s animated works (particularly Cyborg 009 Monster Wars), except for one track from the 1979 series in the climax.
The game ultimately ends with the original intended stop point of the manga, 009 and 002 burn up in re-entering the atmosphere, and two children see them as a shooting star, with the older sister wishing for world peace.