In a remarkably advanced version of 1939, the horizon of New York City witnesses the arrival of the grand zeppelin Hindenburg III, as it moors majestically at the Empire State Building. Amidst this spectacle, a terrified scientist, Dr. Jorge Vargas, finds himself entangled in a web of intrigue as he arranges for two crucial vials to be delivered to Dr. Walter Jennings, only to subsequently vanish without a trace.
Enter Polly Perkins, a determined newspaper reporter for The Chronicle, portrayed by the talented [Gwyneth Paltrow]. She dives headfirst into the investigation of Vargas's disappearance and that of five other eminent scientists. A mysterious message directs her to Radio City Music Hall, and despite the cautionary words of her editor, Paley (played by Michael Gambon), she bravely attends a screening of The Wizard of Oz. It is here she meets Dr. Jennings, who cryptically warns her of impending danger from the enigmatic Dr. Totenkopf. Suddenly, the tranquility of the city is shattered as air raid sirens blare and colossal, indestructible robots unleash chaos.
In a state of urgency, the police summon the legendary "Sky Captain," Joe Sullivan, who leads a private air force known as the Flying Legion. While street-side chaos ensues, Polly captures the dramatic events on camera as Joe incapacitates one of the marauding robots, forcing the rest to retreat. News outlets begin reporting similar attacks occurring worldwide. The wreckage of the robots is taken to the Legion’s base, where the skilled mechanic, Dex Dearborn (Giovanni Ribisi), prepares to examine it. Polly joins Joe, who is not just a colleague but also her former lover; their romantic past traces back to their time together in China.
As they dig deeper, Polly and Joe uncover a ransacked lab belonging to Dr. Jennings, only to discover he is gravely injured during their visit. His assailant, a mysterious woman portrayed by Bai Ling, escapes, but not before Jennings entrusts Polly with the two critical vials, which are key to thwarting Dr. Totenkopf's nefarious schemes. However, Polly chooses to keep this information from Joe.
Upon returning to base, the Flying Legion finds itself under siege from a squadron of Ornithopter drones. As chaos unfolds, Dex manages to pinpoint the source of the robot signal but is captured in the process. Nevertheless, he leaves behind a fragment of a map that highlights Totenkopf's hideout. Determined, Joe and Polly set out for Nepal, leading them into the unexplored depths of the Himalayas. They stumble upon an abandoned mining facility, only to be betrayed by two guides working for Totenkopf, forcing them to surrender the vials and confining them to a room rigged with explosives. The ensuing explosion knocks them unconscious.
Upon regaining consciousness, they find themselves in a fantastical realm known as Shangri-La, where the monks recount the tragic enslavement of their people by Totenkopf, who exploits them for uranium mining. With the last survivor of the ordeal offering vital information about Totenkopf's whereabouts, Polly and Joe turn to Commander Franky Cook, one of Joe’s ex-lovers, who commands a formidable Royal Navy aircraft carrier.
The battle rages as Franky leads an offensive while Joe and Polly delve into an underwater approach. When they finally emerge, Polly notices an amusing detail: the identification number on Joe's plane reads "Polly" when flipped. Their adventure takes a bizarre twist as they discover an island populated with dinosaur-like creatures, ultimately leading them to a hidden underground facility where robots load animals and those critical vials onto a gargantuan "Noah's Ark" rocket.
Caught off guard, Joe and Polly barely escape death thanks to Dex's timely intervention alongside three of the missing scientists. Dex reveals Totenkopf's plan to abandon humanity in favor of creating a new beginning, dubbed the "World of Tomorrow," utilizing the vials as the genetic building blocks for a new Adam and Eve. In the heart of Totenkopf's lair, tragedy strikes as one scientist is incinerated by the automated defenses. A holographic image of Totenkopf, chillingly voiced by Laurence Olivier, provides a frightening glimpse into the mind of a man long-dead but whose ambition persists.
As they uncover Totenkopf’s remains, a note clutched in his hand simply reads, “forgive me.” With the rocket's launch imminent, the team realizes that the only viable strategy is to sabotage it from within. Although Polly is eager to join, Joe takes the harrowing step of knocking her out to ensure her safety while he selflessly prepares to remain behind.
However, fate intervenes as Polly regains consciousness just in time to thwart the mysterious woman, who they discover is a robot. Together, they board the rocket with the tension mounting as they face their last attempt to save humanity. Just before the second stage of the rocket ignites, Joe and Polly manage to eject all animals safely, and Joe cleverly disables the rocket systems. As they make their escape using the last pod, they watch the rocket explode in the distance.
In the aftermath, Joe and Polly witness the animal pods land around their escape vessel. With a sentimental moment at hand, Polly uses her last camera shot to capture Joe's image. He quips about the lens cap being on, leaving her with the sinking realization that she has no evidence of their astonishing adventure.
