As snow falls upon New York City, the Hindenburg III Zeppelin begins docking at the Empire State Building; aboard it is Doctor Jorge Vargas, cradling two tiny silver vials. As the docking process is completed and the passengers prepare to disembark, Vargas approaches an attendent, telling him to deliver a message to a Doctor Walter Jennings. As the attendent walks away, he peers at the message: I am being followed. He is coming for me. Puzzled, the attendent looks back over his shoulder, towards Vargas; the doctor has vanished.
Reporter Polly Perkins (Gwyneth Paltrow) sits at her desk at the Chronicle, hammering out another article on the bizarre disappearances of six scientists. An anonymous package arrives for Polly, containing a book on mathematics and physics, a ticket to a screening at Radio City Music Hall, and an anonymous note reading "I know who is next to disappear. Meet me at 8:00." On her way out the door, she is stopped by her editor, Mr. Paley (Michael Gambon), who pleads with her not to get embroiled in the clearly clandestine and potentially dangerous plot behind the disappearances. Polly's appetite for the story is too strong, and she promises to bring Paley some popcorn.
During a screening of "The Wizard of Oz," Polly sits with an older Germanic man of speaks of a group of seven scientists called Unit Eleven, who conducted unspoken of experiments in Berlin prior to the outbreak of the Great War. With the man clearly frightened, Polly pushes him to tell him who is next; the says, why of course, he is - the last remaining member of Unit Eleven. Polly doesn't understand who would be capable of absconding with the entirity of Unit Eleven - who could be behind all of this? The scientist - Jennings - replies only "Totenkopf." As the mutters the name, the air raid sirens blare outside. The patrons flee the theatre, but Polly notices a few documents Jennings has dropped.
An immense squadron of towering robots descends upon New York, making their way towards downtown's central generators. Polly quickly dives into the line of fire, eager to snap some photographs, and ends up dodging the barrage of debris and the enormous, crushing gait of the sentry's feet as they march through the New York avenues. The police attempt to take them out via Thompsons, but the bullets riccochet harmlessly off the metal titans. Clearly an emergency, the call is put out for Sky Captain.
Hurtling into New York, Sky Captain begins an assault on the robots, but finds them quite impervious to his weapons. They seem to hardly notice his gun fire, nor does snaring them in lengths of chord hinder their movement. Resorting to planting a bomb on a sentry's leg, the robot is felled, and the rest stop immediately and take flight, retreating. Even from high above, Sky Captain sees Polly amidst the rubble, and just as he recognizes her, she recognizes him. It seems they have a history.
The New York attack was hardly an isolated incident, however; newspapers show attacks in Berlin, South America, Tokyo, Moscow. A worldwide onslaught from the legions of mechanized soldiers.
Though leaving the generators in tact, the felled robot is swept back to Sky Captain's - whose name is Joe Sullivan - island headquarters, where his top mechanic and scientist buddy Dex (Giovanni Ribisi) promises to take it apart, see what makes it tick, just as he fine tunes a metal-metaling heat ray pistol. Dex finds that a signal is emitted to control the units, and if they can trace the coordinates of the signal, they can find their culprit. Joe retreats to his office and downs a quick shot of milk of magnesia before he notices he has company; Polly has arrived, unannounced, after three years. The two parted on bad terms; in Nanking, Joe's plane was sabotaged and he thusly spent three months in a Manchurian prison camp, and blames Polly, who equally believes Joe was running around on her the entire time. Both vehemently deny it, and Joe wants nothing in the way of reconciliation. Before Polly is escorted off the premises, she reveals the document Jennings dropped in the theatre - blue-prints to the robotic sentries, and the name "Totenkopf." Realizing they need each other, they agree to a truce; Joe gets access to what she knows, but Polly gets to come along for the story of a lifetime.
Dex and Joe lead Polly to a hangar surprisingly full of the ruined sentries. Dex recalls the robots have been appearing in remote areas, rampaging and retreating almost as quickly. They've still no clue as to their whereabouts or origins.
Polly and Joe agree to pay Dr. Jennings a visit, try to find out more about the mysterious Totenkopf; arriving at his office/laboratory (adorned with the numbers "1138," a less-than-subtle reference to George Lucas), they find they've been beaten to the punch. The office has been ransacked, and find Jennings on the verge of death. Jennings barely gasps to Polly that Totenkopf must not get these vials, for if so, the countdown begins and our world is doomed. Quietly handing the silver vials to Polly, she tucks them away as Joe finds a mysterious hooded woman (Bai Ling) rummaging through Jennings' files. Joe tries to talk to her, but the Mysterious Woman shows not only amazing prowess and strength, but also weaponry; her staff emits a powerful beam that nearly incinerates Joe's head. The Mysterious Woman flees, leaving behind the documents Jennings had. As Polly and Joe prepare to leave, the air raid sirens sound, and they must rush back to the base.
At the island headquarters, a squadron of bat-like airships fly in formation towards the base. Scrambling to get airborne, Polly joins the reluctant Joe, while Dex reminds him that they have to find and track the control signal to the automatons. As the attack begins and the bat airships decimate the headquarters in waves of strife, Dex radios Joe to tell him only one ship is emitting the signal, and unless they can figure out which one it is, he must not open fire. Finding the signal ship, Joe tries desperately to stay close enough to read the signal so Dex may follow. The airships break off and head towards New York with Joe in hot pursuit, following some misguided shortcut advice from Polly, ever the backseat pilot. Just as Dex tracks the signal to an uncharted area in Nepal, sentries burst through the base walls, capturing and kidnapping Dex. Still struggling to get the airships off his tail, Joe plunges his plane into the ocean as Polly fully expects to die; turns out Joe's plane is amphibious, and as the sentry airships hit the water's surface, they each break up into a fiery burst. Joe and Polly head back to base.
Finding the base in ruins and no sign of Dex, they search for clues, seeing the escape of the Mysterious Woman and her robotic soldiers. Unable to stop them, Joe does discover the sliver of map Dex has placed on a wall via his omnipresent Dubble Bubble gum - "X" marks the Nepalese site from which the signal is being transmitted.
On their way to Nepal, Polly rummages through Jennings' files, finding some history on Unit Eleven and Totenkopf; brilliant from even a young age - his first patent at 12 - Totenkopf was the leading scientist of Unit Eleven, constantly escorted by none other than the Mysterious Woman. Totenkopf vanished, only to resurface thirty years later as the scientists began to vanish.
In Nepal, Joe meets up with his friend Kaji, who, along with two Chirpas, will lead them to the site of Totenkopf's citadel - deep within the region of Nepal thought to be Shangra-La. Arriving there, they discover an enormous empty citadel and a nearby abandoned mining facility, poisoned with uranium. Without warning, Joe and Polly are betrayed by the two Chirpas, locked inside a room stocked with dynamite. Unwittingly saved by a completely unaware Kaji, the three barely make it out of the mining cavern as it fills with fire. The Mysterious Woman oversees the destruction from a nearby cliff, marching triumphantly into her airship. Unbeknownst to her, the trio has survived.
Waking up in a Shangra-La bed - naked, and next to an equally disrobed Polly and Kaji - Joe tells their attendent they search for Totenkopf so that they may destroy him. Promising him help, as Totenkopf poisoned the people of Shangra-La by forcing them to toil away in the contaminated mine, he shall guide Joe to the last remaining survivor of Totenkopf's wretched cruelty. Irridated and monstrous, the dying man gives a small staff to Joe as a guide with which to find Totenkopf, but asks for only one wish. As Joe leans towards him, the frail man whispers, "kill me." Joe's resolved is steeled.
Departing, Joe figures out that the staff is a sort of astrological guide used in conjunction with nautical navagation to calculate a specific latitude and longitude, placing Totenkopf's stronghold smackdab in the middle of nowhere, not even existing on a map. Low on fuel, Joe calls in to old friend and British operative Lt. Franky Cook (Angelia Jolie, whose character is only a cigar and a few white streaks away from Nick Fury). Landing on Franky's enormous helipad/mobile carrier, Joe gives her the coordinates of Totenkopf's man-made island and tells her his plan to get inside. Polly is steaming from discovering Franky is a female, and burns as Frankie calls her "the competition." Agreeing the best way into Totenkopf's is via an underwater duct, Frankie prepares the amphibious Manta squadron as they near the island and face a bevy of anti-aircraft fire and defense.
Delving into the ocean, Joe, Frankie, and the Manta Squadron are equally confronted with enormous, crab-like sentries who fire bursts of torpedos. Polly, however, could care less, as she is sure it is with Frankie whom Joe was cheating with in Nanking. Barely managing inside a duct, Joe pilots his ship onto the island, where he and Polly find a lush jungle island populated by almost prehistoric animals created by Totenkopf's bizarre engineering. Making their way through the jungle, Polly opines that her camera has only two exposures left, which is more than frustrating considering this story is getting bigger and bigger quickly. As the two outrun an enormous pterodactyl, Polly sobs; she's accidently clicked an exposure and shot a photo of the ground as she ran. Joe can't help but laugh.
The two stop, and Polly confesses she sabotaged Joe's plane. Joe confesses he ran around with Frankie in Nanking. The two move on.
At the foot of an ancient temple, Joe and Polly make it inside Totenkopf's mountain, which houses an enormous rocket. Totenkopf is loading two of each animal into the giant rocketship, an ark of some sort; for what purpose, neither knows. Polly foolishly alerts the hovering sentries to there presence, and are suddenly beset upon by the guards and the supervising Mysterious Woman. They are saved at the last moment by Dex and three escaped scientists, who have commandeered a vehicle and manage to outrun the hovering robots. They explain that Totenkopf intends to launch the rocket into space, carrying two of each animal within it - the twin vials actually contain the basic seeds of human life, hence their importance. Once the rocket reaches 100 kilometers, a device will trigger and incinerate the Earth, allowing the human race to start over anew.
Dex takes them to Totenkopf's office, which is guarded by two towering robotic guards. Joe quickly fells them with Dex's metal-melting heat ray pistol. One of the doctors foolishly tries to make haste through the doors to Totenkopf himself, but upon stepping on a metal pad flanked by towering tesslacoils, he is thoroughly electrocuted and reduced to smoldering bone. An enormous computer-generated visage of Totenkopf (comprised of stock footage and audio of the deceased Sir Laurence Olivier), who explains that his intent is merely to allow the human race to rid itself of the overpowering hatred and violence that has become endemic, to start anew fresh, for the site of man's own inhumanity is all together intolerable. Dex hotwires the coils and allows them entrance, finding the office empty. Totenkopf's personal papers are there - but evidently not the man himself.
Joe, however, finds Totenkopf. Nearly mummified, Totenkopf's lifeless corpse sits in a chair overlooking the construction and loading of the Rocket-Ark. He grasps a note that simply reads, "Forgive Me."
The scientists find that a key wire must be cut inside the rocket itself, but that by doing so, the detonation process would be sped up and not allow time for escape. Agreeing to go, Joe knocks Polly unconscious to ensure she doesn't follow and tells Dex to contact Frankie as soon as they get off the island.
Joe races towards the rocketship as it finalizes loading, only to be met by the fierce Mysterious Woman, who bears a bo staff-like weapon in appropriately Darth Maul-esque style. Joe is quickly overcome by her strength and grace, but the Woman is felled by a swift smack to the face courtesy Polly, who jumped off the hovercraft with Dex and the remaining scientists when no one was looking. It turns out the Woman was just another one of Totenkopf's robots, and Polly and Joe head aboard the rocket.
Making their way to the top level, Polly strikes the emergency release button, was drops all of the captive animals into the ocean in protective, cushioned, parachute-adjoined capsules. Reaching the core, they are at the last minute detained by the still kicking Mysterious Woman, whose crushed face reveals her robotic form. Joe strikes her with her own electric staff, then uses it to short out the controls and cause the Ark to detonate. Just before the explosion, a serious of corridors open, and Joe explains he believes it may be their ticket to freedom.
As Dex and the scientists watch the Ark burst to smithereens in middair, Joe and Polly's capsule lands in the ocean. Set against a beautiful orange backdrop, the island is populated by parachuting capsules, loose animals, and the smoky debris of the Ark hovering in the dusk sky. Quickly framing the breath-taking tableau in her viewfinder, she prepare to snap the picture - only to pan over to Joe watching it all. She snaps a photo of Joe, who looks at her astounded. She begins to reassure him, but Joe replies ...
"No, Polly ... it isn't that ... Polly - your lenscap ... ?"
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