When a mysterious beam of light starts disrupting and destroying the Earth's atmosphere, Flash Gordon, Dr. Zarkov, and Dale Arden - accidentally accompanied by wisecracking reporter Happy Hapgood - swing into action in Zarkov's rocketship, believing that it could be coming from the planet Mongo.
Once in space, however, they discover that the ray is originating from Mars. Journeying to the fourth planet, they discover that their old enemy from Mongo, Ming the Merciless, whom they had believed dead, is still alive, and has formed an alliance with Azura, the Witch Queen of Mars.
From Azura's planet, and under her protection, he is operating a gigantic Nitron ray that is destroying Earth's atmosphere. Azura's powers include the ability to transmute people into figures of living clay, condemned to live in darkened caves, and she is hated and feared by most of the population.
Conversely, the Clay People, led by their King, know the secret of how to eliminate Azura's power, but lack the means of escaping the caves to which their ruined bodies restrict them, in order to battle her. Gordon and his party would seem to hold the answer to their problem, except that the Clay People don't trust them at first, and end up holding Dale Arden hostage.
Ultimately the Earth visitors and the Clay People become allies in the tandem quest to defeat Azura and stop Ming from destroying the Earth. Flash, Dale, Zarkov, and Hapgood do battle against Azura's magic and her Martian space-force, Ming's super-scientific weaponry, the treacherous Forest People, and other dangers on the Red Planet.
Finally, they win by the classic strategy of divide-and-conquer, showing Azura that Ming has been plotting behind her back to take power from her. Azura's alliance with Ming is broken, at the cost of the Queen's own life, but the Clay People are freed from their curse. And the evil emperor of Mongo, his Nitron ray destroyed and his escape cut off on all sides by the now hostile Martian forces, is finally destroyed by the accidental result of his own machinations and treachery.
This serial, the first sequel to Flash Gordon, was based on the 1936 "Big Little Book" adaptation of the strip "Flash Gordon and the Witch Queen of Mongo". According to Harmon and Glut, the location was changed to Mars to capitalise on Orson Welles' famous War of the Worlds broadcast. According to Stedman, this serial preceded that broadcast, which made Universal hastily release a feature version of the serial as Mars Attacks the World to capitalise on the publicity. The film was a box office success.
Universal Pictures also prepared a feature length edited version of this serial, which was already in print and ready for release in October 1938 when Orson Welles astounded the country with his Mercury Theatre on the Air radio production of H. G. Wells's The War of the Worlds. As an exploitation film tie in, Universal had the feature's title changed to Mars Attacks the World, and a week after the Welles broadcast, opened it at a Broadway theater as a major premiere event.
The original title for this feature had been Rocket Ship, which was subsequently added to reissues of the first Flash Gordon serial's feature version, shown under its source serial's title in 1936. Time magazine declared the serial to be "a Grade A cinemedition of the famed King Features strip."