In 1957, Soviet agents working under Irina Spalko kidnap Indiana Jones and his partner George “Mac” McHale. The Soviets infiltrate a secret government warehouse, located in Nevada, labeled “Hangar 51“, and force Jones to locate a mummified corpse from the Roswell UFO incident, which he was forced to work on ten years earlier. Shortly after retrieving the corpse, Mac reveals he has become a double agent on the KGB’s payroll. Jones unsuccessfully attempts to steal the body, and fights with Spalko’s henchman Dovchenko, before escaping to a nearby model town right before an atomic bomb test. He takes shelter in a lead-lined refrigerator, and FBI agents eventually rescue, decontaminate, and interrogate him, suspecting him of working for the Soviets. Though eventually freed, Jones is put on an indefinite leave of absence from Marshall College, and the dean resigns to spare Jones from being fired.
Greaser Mutt Williams approaches Jones, notifying him that Jones’ former colleague, Professor Harold Oxley, found a crystal skull in Peru, but has since been kidnapped along with Mutt’s mother, Marion, who went after him. Jones tells Mutt of the legend of crystal skulls found in Akator, and Mutt gives Jones a letter from his mother, which contains a riddle from Oxley in an ancient language. Two Soviet agents attempt to capture them, but Jones and Mutt escape and, following the riddle’s meaning, reach Peru. At the local psychiatric hospital, carvings on the walls and floor of Oxley’s cell lead them to the grave of Francisco de Orellana, a Conquistador who searched for Akator. They find the skull at the grave, and Jones reasons that Oxley had returned it there. While the two are departing the tomb, Mac and the Soviets take them hostage and deliver them to their camp in the Amazon jungle. There, the pair find an addled Oxley and Marion, who is revealed to be Marion Ravenwood, an old partner of Jones’; she reveals to Jones that Mutt is his son.