In an alternate, more technologically advanced 1939, the zeppelin Hindenburg III arrives in New York City, mooring at the Empire State Building. A frightened scientist named Dr. Jorge Vargas (Julian Curry) makes arrangements for a package containing two vials to be delivered to a Dr. Walter Jennings (Trevor Baxter), then vanishes.Polly Perkins (Gwyneth Paltrow), a newspaper reporter for The Chronicle, looks into the disappearances of Vargas and five other renowned scientists. She receives a cryptic message telling her to go to Radio City Music Hall. Ignoring the warning of editor Paley (Michael Gambon) not to go, she meets Dr. Jennings during a showing of The Wizard of Oz. He tells her that Dr. Totenkopf is coming for him. Suddenly, air raid sirens go off as giant indestructible robots attack the city. In desperation, the police call for "Sky Captain" Joe Sullivan (Jude Law), who commands a private air force based in New York, the Flying Legion.Polly photographs the action from the street as Sullivan knocks out one robot and the rest leave. News reports show similar attacks around the globe. The robot's wreckage is taken back to the Legion's air base so that its expert, Dex Dearborn (Giovanni Ribisi), can examine it. Polly follows, hoping to get information for her story. She and Joe are ex-lovers, who broke up three years earlier in China where Joe was serving with the Flying Tigers. Since it appears Polly has useful information, Joe agrees to let her in on the investigation. Her lead takes them to the ransacked laboratory of Dr. Jennings, with the scientist himself near death. The killer, a mysterious woman (Bai Ling), escapes. Jennings gives Polly two vials, which he says are crucial to Dr. Totenkopf's plans. Polly withholds this information from Joe. They return to the Legion's base, which comes under attack from squadrons of Ornithopter drones. Dex manages to track the origin of the robot control signal, but he's captured. However, he leaves behind a part of a map marking the location of Totenkopf's base.Joe and Polly find it and head to Nepal. Venturing into the Himalayas, they discover an abandoned mining outpost. Two guides turn out to be working for Totenkopf, forcing Polly to turn over the vials and then locking her and Joe in a room full of explosives, which they light. Joe and Polly are knocked unconscious by the explosion. They wake up together in the mythical Shangri-La. The 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 (who was suffering from radiation poisoning) provides a clue to where Totenkopf is hiding. This leads them to another of Joe's ex-flames, Commander Franky Cook (Angelina Jolie), who commands a Royal Navy flying aircraft carrier with submarine aircraft.Franky leads the attack while Joe and Polly enter through an underwater inlet. After surfacing, Polly notices that the identification number on Joe's aircraft reads "Polly" when viewed upside-down. Joe and Polly find themselves on an island with dinosaur-like creatures. They head to a mountain and find a secret underground facility, where robots are loading animals, as well as the mysterious vials, onto a large "Noah's Ark" rocket. Joe and Polly are detected and nearly killed. Dex, piloting a barge, arrives in the nick of time with three of the missing scientists. Dex explains that Totenkopf has given up on humanity and seeks to start the world over again: the "World of Tomorrow". The vials are genetic material for a male and female human: a new Adam and Eve.In Totenkopf's lair, one scientist is incinerated by the defense system. A holograph of Totenkopf (Laurence Olivier) appears and speaks. Dex disables the defenses, and the group discovers Totenkopf's mummified corpse. He had died 20 years before, but his machines have carried on his work. In his hand is a scrap of paper reading "forgive me". The only way to sabotage the rocket is from the inside. Polly tries to tag along, but Joe kisses her and knocks her out. He prepares to sacrifice himself while the others escape. Polly recovers and follows Joe, arriving in time to save him from the mysterious woman, who turns out to be a robot. The two board the rocket. Before it reaches 100 km, when its second stage fires and incinerates 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 robot. He jolts her with her electric weapon and then uses it on the controls, disabling the rocket. They use the last pod to save themselves as the rocket safely explodes.Joe and Polly watch the animal pods splash down around their escape pod. Polly then uses the last shot on her camera to take a picture of Joe. He tells her that the lens cap was still on the camera. Polly's look of joy turns to shock as she realizes she has no proof any of their adventure happened.