Circa 1939 ace city reporter Polly Perkins has noted the sudden disappearances of many of the world's most famous scientists. After the city falls under attack of giant flying robots, she decides to team up with her ex-boyfriend, aviation officer Joe 'Sky Captain' Sullivan and flys around the world in search of the evil mastermind, Dr. Totenkopf, whose plan it is to create a new world by destroying the one of today.