Plot
In a technologically advanced New York City in 1939, the zeppelin Hindenburg III moors itself atop the Empire State Building. Aboard the airship is Dr. Jorge Vargas, a scientist who arranges for a package containing two vials to be delivered to Dr. Walter Jennings. Afterwards, Dr. Vargas vanishes.
Polly Perkins, a reporter for The Chronicle, is looking into the disappearances of Vargas and five other renowned scientists. A cryptic message leads her to Radio City Music Hall, against the warnings of her editor, Mr. Paley, where she meets Dr. Jennings during a showing of The Wizard of Oz. He tells her that a Dr. Totenkopf is coming for him next. Suddenly, mysterious giant robots attack the city. The authorities call for "Sky Captain" Joe Sullivan, the city's hero, Perkins' former lover, and the commander of the mercenary air force the Flying Legion. While Joe engages the robots with his modified Curtiss P-40 pursuit fighter, Perkins photographs from the street with little regard for her safety. He disables one robot; the rest leave. News reports show similar attacks around the globe. The disabled robot is taken back to the Legion's air base so that technology expert Dex can examine it. Polly follows and persuades Joe to reluctantly let her in on the investigation.
She discovers Dr. Totenkopf was a former child prodigy and Germany's most brilliant scientist who ran a mysterious lab outside of Berlin where he and the missing scientists were working on a project dubbed the "World of Tomorrow". Her information takes them to the ransacked laboratory of a dying Dr. Jennings, while an assassin escapes. Just before he dies, Jennings gives Polly the two vials and states that they are crucial to Totenkopf's plans. Polly hides the vials and withholds the information from Joe. They return to the Legion's base just before it comes under attack from squadrons of ornithopter drones. Dex tracks the origin of the signal controlling the drones and notes it on a map before his capture.
Joe and Polly find Dex's map and fly to Nepal and then Tibet, where they meet Joe's old friend Kaji. He helps them locate an abandoned mining outpost in the Himalayas. Two guides working for Totenkopf force Polly to turn over the vials, locking the duo in a room full of dynamite. Joe and Polly escape just before the room explodes, knocking them unconscious and destroying most of Polly's film. They wake up together in the mythical Shangri-La. The Tibetan-speaking monks there tell of Totenkopf's enslavement of their people, forcing them to work in the uranium mines. Most were killed by the radiation, but the final survivor provides a clue to where Dr. Totenkopf is hiding.
With insufficient fuel to make it there, they run into a Royal Navy flying aircraft carrier commanded by another of Joe's former flames, Commander Franky Cook. Franky leads the attack on Totenkopf's island lair while Joe and Polly enter through an underwater inlet. Joe and Polly find themselves on an island with dinosaur-like creatures, which Polly hesitates to photograph as she has only two shots left. They find a secret subterranean facility in a mountain, where robots are loading animals, as well as the mysterious vials, onto a large "Noah's Ark" rocket. Joe and Polly are detected but Dex, piloting a flying barge, arrives with three of the missing scientists. They explain that Totenkopf has given up on humanity and seeks to start the world over again: the "World of Tomorrow". The vials are genetic material from humanity's greatest individuals which will produce the perfect Adam and Eve. If the rocket reaches space, the afterburners will ignite the atmosphere and kill everything on Earth, before the rocket repopulates the planet in Totenkopf's image.
As the group attempts to enter Dr. Totenkopf's lair, one scientist is electrocuted by the defense system. A hologram of Totenkopf appears, speaking of his hate for humanity and his plans to rebuild it as a new master race. Dex disables the lair's defenses and the group discovers Totenkopf's mummified corpse inside with a scrap of paper clutched in his hand: "forgive me". He died 20 years previously, but his machines have continued his plan. Joe decides to sabotage the rocket from the inside while the others escape. Polly tries to tag along but Joe kisses her and then knocks her out. Polly recovers, following Joe and saving him from Dr. Jennings' assassin, a female android. Joe and Polly then board the rocket. Before the rocket reaches 100 km, when its second stage is scheduled to fire and thereby incinerate the Earth, Polly pushes an emergency button that ejects all the animals in escape pods. Joe tries to disable the rocket only to be interrupted by the same assassin robot. He jolts the robot with its electric weapon and then uses it on the controls, disabling the rocket. Joe and Polly use the last pod to save themselves as the rocket explodes. Joe and Polly watch the animal pods splash down around their escape pod, while Commander Cook leads a group of flying aircraft carriers towards them. Polly then uses the last shot on her camera to take a picture of Joe rather than the animal pods. Joe notes that she had forgotten to take the lens cap off.
