The story of Cyborg 009 revolves around nine young people who were turned into cyborgs by a company seeking world domination. They have since defeated the company and now use their powers to protect the world.
The gameplay in Cyborg 009 is an action-adventure side-scroller, where the player controls one of eight cyborgs, utilizing their unique abilities to complete various missions. Each cyborg has distinct powers: 002 can fly and hover; 003 can see in the dark; 004 can fire bullets from his fingers and rockets from his knees; 005 can break rocks with his fists; 006 can blow fire that also melts rocks; 007 can change shape to mimic enemies; 008 can swim underwater for extended periods; and 009 can move at incredibly high speeds. Using these abilities consumes SP, which slowly regenerates.
Additional attributes govern the cyborgs' attack and defensive powers, their amount of SP, and how quickly SP regenerates. Before each mission, a leader is chosen, and two more cyborgs can be selected by the player. The game allows for switching between cyborgs at any time, despite only one being controllable at a time.