The public knows of government agencies like the FBI and CIA, but little is known of this super-secret agency. Code-named "Elite Beat Agents", these men in black are heroes' heroes and the coolest group of guys this world has ever known. Of course, according to official records, they do not exist. Their leader, an ex-CIA agent named Commander Kahn, scans the world for cries of help. When he finds one, he dispatches the agents, who assist their targets by performing a song and dance. The hypnotic nature of their rocking revives the targets with "Groovy" energy that boosts their willpower and helps them overcome their obstacles. In each stage, the agents arrive in a special "Beat Transport" and must tap and trace patterns that appear on-screen to the beat of the music to save the day.