The film begins with a video documentary by Dr. David Kruipen (Val Kilmer), a research scientist on Banks Island, in the Canadian Arctic and the outbreak of a pandemic, with 400 dead and 10,000 infected. This is followed by a flashback to when David, his assistant Jane (Anne Marie DeLuise) and two other researchers tranquilize a polar bear, then discover the frozen remains of a woolly mammoth. They transport the polar bear to their research station. David calls his daughter Evelyn (Martha MacIsaac) and pleads with her to visit the research station. Their relationship has been strained since the recent death of her mother. Meanwhile, a group of students, Ling (Steph Song), Federico (Kyle Schmid) and Atom (Aaron Ashmore), are selected to join David's research team; Evelyn decides to come. Days later, David's research team begins feeling the effects of a strange illness, and David tells helicopter pilot Bart not to bring his daughter Evelyn to the station. However, Evelyn insists, leaving Bart no choice but to bring her to the station along with the students. In the meantime, Jane shoots and apparently kills David and another researcher. The students discover the body of the polar bear, and Bart is bitten by a bug while touching it. Evelyn is awakened in the middle of the night by an all-terrain vehicle approaching the station. When Evelyn investigates, she discovers Jane in the helicopter. Jane has destroyed the helicopter's control panel, eliminating any immediate chance of escape. Ling wakes up with many bug bites on her face and torso, and Jane dies in Evelyn's arms. Realizing Ling is sick, Federico calls in a helicopter to rescue Ling. Attempting to find David, Evelyn and Atom discover eggs in the brain of the mammoth. Assuming her father has been infected, Evelyn and Atom deduce that something has made the group sick. Evelyn decides to cancel the rescue helicopter and quarantine the group until a better-prepared team can rescue them. Federico, discovering he too is infected, goes berserk and destroys the radio. The bite on Bart's arm is infected and he has Atom and Evelyn amputate his arm at the elbow. The group decides to destroy the facility and wait things out in the helicopter. Ling is attacked by bugs who have made their way in through the ventilation system. Bart discovers that the amputation was useless as his upper arm is now showing signs of infection; he opts to stay behind with Ling. They deliberately overdose on morphine and fall asleep as the bugs swarm over them. Federico comes running out, refusing to be checked for infection, then turns on Evelyn and Atom. As he is about to shoot Evelyn, he is shot from behind by David. David insists they destroy the research station. Evelyn finds a video David recorded and discovers that David has intentionally infected himself, preparing to set the bugs loose to teach humanity a lesson about global warming 's effects. As a rescue helicopter comes to pick up David, Evelyn and Atom are locked up by David, but they escape. Atom grabs one of the helicopter’s skids to attempt to make the helicopter land, but falls to the ground after being shaken off by the pilot’s attempts to stabilise it, and is mortally injured. As the helicopter starts flying away, Evelyn shoots at it, causing it to crash into a building previously doused in gasoline. David and the helicopter crew die in the resulting fire; Evelyn finds Atom, who dies in her arms. The following day another rescue team arrives, finding the destruction and Evelyn, the sole survivor. Later, as a radio station airs information based on Evelyn's reports, a hunter calls his dog away from a dead bird the dog has been eating. Bugs emerge from the bird's body, which was infected from eating the mammoth. The closing scene shows the hunter's truck heading towards a large city.

During an expedition into Central Africa, paleontologist Dr. Susan Matthews-Loomis and her husband George Loomis attempt to track down evidence of a local monster legend. The monster, which the local natives refer to as " Mokele-mbembe ", shares many characteristics with the Sauropod order of dinosaurs. During the expedition, they discover brontosaurus in the deep jungle and are further amazed when the animals show very little fear of them. The couple begins observing the creatures and become especially enamored with the curious young offspring of the pair, whom they nickname "Baby". Unfortunately, the discovery soon places the dinosaurs in jeopardy from both the local military as well as fellow scientist Dr. Eric Kiviat. Whereas Dr. Kiviat sees Baby and his parents as his ticket to fame and fortune, the African military led by Colonel Nsogbu sees the dinosaurs as a threat and makes several attempts to destroy them. During one such attempt, the adult male brontosaurus is killed and the adult female captured. The Loomises are able to escape with Baby, but quickly find themselves lost in the jungle while being pursued by Colonel Nsogbu's forces. After finally escaping their pursuers, the pair decide to circle back and rescue the female adult brontosaurus, whom Dr. Kiviat has persuaded Colonel Nsogbu to transport back to civilization. With the aid of the local tribe – who see Baby and his parents as legends – George and Susan are able to break into the military compound and release the mother brontosaurus. During the escape, both Kiviat and Nsogbu are killed. Afterwards, the Loomises take the pair to a secluded jungle lagoon and say a tearful goodbye to Baby as he follows his mother away into the deeper parts of the jungle.

Akademik Vladislav Volkov, a Russian research vessel in the South Pacific, communicates with the orbiting space station Mir. An energy source traveling through space strikes Mir, killing the cosmonauts and beaming itself down to Volkov. The electrical surge takes over the ship and attacks the crew. Seven days later, the tugboat Sea Star, captained by alcoholic Robert Everton, loses its uninsured cargo while sailing through a typhoon. Sea Star 's crew discover the engine room taking on water. When Sea Star takes refuge in the eye of the storm to make repairs, Volkov appears on their radar. Realizing that it could be worth millions in salvage, Everton orders his crew aboard. On Volkov, most of the electronics have been destroyed and the Russian crew are seemingly missing. Everton orders Sea Star 's navigator and ex- Navy officer Kelly Foster to help a fellow crewman, Squeaky, restore power to the ship. The ship's anchor then drops on its own, sinking Sea Star with deckhand Hiko and first mate J.W. Woods Jr. on board. Sea Star 's engineer Steve Baker leaves Squeaky to guard the engine room, where a robotic creature lures him to his death. Steve rescues an injured Hiko, while Woods comes out unscathed. As Foster treats Hiko in the sick bay, Chief Science Officer Nadia Vinogradova, the sole surviving member of Volkov 's crew, shoots at the crew before Steve subdues her. Nadia is hysterical about "it" needing power to travel through the ship and implores the crew to shut down the generators. She attacks Everton and Foster, who subdue her and take her to the bridge. Steve, Woods, and crewman Richie Mason look for Squeaky in the engine room but instead stumble upon an automated workshop producing more robots. The three are attacked by the robots and what appears to be a gun-wielding Russian crew member. The Russian is revealed to be a cyborg, but the three bring it down with salvaged munitions from Volkov 's small arms locker and take its seemingly dead body to the bridge. Nadia explains that the sentient electrical energy beamed from the Mir took over the ship eight days prior, scanned the ship's computers to find information on killing humans, then used the automated workshops to convert Volkov' s crew into cyborgs; the one brought to the bridge was the ship's captain and Nadia's husband. As the storm resumes, the crew head for the computer room. En route, they are ambushed by a converted Squeaky and a giant robot that kills Woods. The survivors barricade themselves in the communications room. Richie sends out a mayday, but Everton shoots out the radio, unwilling to give up his salvage. Foster punches Everton and removes him from command. Richie uses the computers to talk to the alien; it says that it is "aware" and sees mankind as a "virus" which it plans to use as "spare parts." This drives Richie insane, causing him to gun down Squeaky and flee. When the remaining crew leave the room, Everton talks to the alien, which recognizes him as the "dominant lifeform." The crew discovers that the alien has moved Volkov ' s computer elsewhere in the ship. Realizing that Volkov is moving, they return to the bridge by going outside, where Hiko is lost to the typhoon. Meanwhile, Everton is guided to one of the workshops, where he makes a bargain with the alien. Foster identifies Lord Howe Island as Volkov' s destination, with Nadia surmising that the alien wishes to seize a British intelligence station from which it could seize control of the world's military forces. As they decide to sink Volkov, the survivors are confronted by the now-cyborg Everton, which they defeat with a thermite hand grenade. They empty Volkov 's fuel tanks and set explosive charges. Foster, Steve and Nadia run into Richie. A giant robot (piloted by the alien) then appears and attacks the trio. The alien captures Foster and tortures her for the detonator's location. A mortally wounded Richie informs Steve that he prepared a jury-rigged ejection seat that can be used for escape. Nadia and Steve rescue Foster, and Nadia sacrifices herself by shooting a flaregun at nearby gas tanks to kill the alien; however, it is only damaged by the explosion and pursues the survivors. Foster and Steve use Richie's ejection seat, escaping the robot form, which triggers pin grenades causing an explosion of the missile bomb and sinks Volkov, causing the sentient electricity to disperse in the seawater. A U.S. naval ship later rescues Foster and Steve.

In the distant future, an overcrowded and troubled Earth relies on research conducted by scientists in remote stations across the Solar System. Contact is maintained by spaceships shuttling between the stations and large orbiting space stations. Captain James is preparing to depart from one of these stations around Saturn when he is murdered by Captain Benson. Benson, who was rated "potentially unstable" on a mental exam, then departs from the station using his cargo ship for a small, remote experimental hydroponics research station called Saturn 3. Arriving there, he finds the station run solely by Adam and his younger colleague and lover, Alex. Adam, Alex, and their dog, Sally, enjoy their isolation away from Earth. Alex has spent her entire life in space and knows Earth only from what Adam has told her. It falls to Benson to more fully educate Alex as to the habits and mores of humans who live on Earth, which include drug use. Alex and Adam's idyll is broken when Benson reveals his mission is to replace at least one of the moon's scientists with a robot. The robot—named Hector—is among the first of its kind, a "Demigod Series" model that relies on "pure brain tissue" extracted from human fetuses and is programmed via a direct link to Benson's brain. Adam tells Alex that he is the likely candidate for removal, being that he is close to "abort time" and will have to leave anyway. With Hector assembled, Benson begins preparing the robot, using the neural link implanted in his spine. Thus connected to Benson, Hector quickly learns of Benson's failure of the psychological stability test, and also of his murder of James. With little barrier between the robot's brain and Benson's, Hector is soon imbued with Benson's homicidal nature and his lust for Alex. The robot rebels. Adam and Benson disable the robot while it is recharging and remove its brain. Believing the danger is over, Adam accuses Benson of gross incompetence and orders him to dismantle the robot and return to Earth when the eclipse ends (the eclipse also prevents communication with other stations). Unknown to Benson, Adam, and Alex, Hector remains functional enough to take control of the base's older robots and use them to reassemble his body and reconnect his brain. Unaware of Hector's resurgence, Benson attempts to leave the station while dragging Alex with him. Resuscitated, Hector murders Benson before he can leave with Alex. Hector destroys Benson's spacecraft before the scientists can escape in it, trapping them all on Saturn 3, and assumes control of the station's computer. Trapped in the control room, both Alex and Adam are surprised to see Benson's face on their monitor. The two are directed by a voice they recognise as Benson's to leave the control room, both surprised that Benson is even alive. To their shock, the two are confronted by Hector, now wearing Benson's severed head. A short time later, Alex and Adam wake in their own rooms. To her horror, Alex finds that Hector has installed a brain link at the top of Adam's spine, much like the one that Benson had, and one which will give Hector direct access to Adam's brain. Hector explains that he can 'read' but taking control of Adam 'comes later'. This causes Adam to rebel, and he destroys Hector by tackling him into a waste pit and sacrificing himself with a grenade. In the final scene, Alex is shown aboard a passenger ship returning to Earth. She declines an offer of narcotics from a stewardess and instead looks out of a window for her first glimpse of Earth.

In the near future, the U.S. Navy develops the F/A-37 Talon, a single-seat strike fighter with advanced payload, range, speed, and stealth capabilities. The program recruits three pilots out of 400 applicants; Lieutenants Ben Gannon, Kara Wade, and Henry Purcell. Captain George Cummings is the overall head. To further advance the program, Cummings has an artificial intelligence, the " Extreme Deep Invader " (EDI), installed on an autonomous aircraft. EDI joins the others on the USS Abraham Lincoln in the Philippine Sea to learn combat maneuvers from the pilots. This sparks controversy over a machine's inability to make moral decisions versus the human struggle to overcome ego. While training EDI in air combat maneuvers, the team is unexpectedly reassigned to kill the commanders of three terrorist cells at a conference in downtown Rangoon. According to EDI's calculation, minimum collateral damage can only be achieved by a vertical missile strike augmented by the bomber diving at a speed sufficient to cause a human pilot to black out. Command authorizes EDI to attack, but Gannon defies orders and carries out the attack himself, blacking out and regaining consciousness just in time to avoid crashing. As the team returns to the Lincoln, EDI is hit by lightning. Subsequent inspection of EDI reveals an accelerated learning pace and development of a rudimentary ethical code and an ego, which might lead to unpredictable behaviors, but Cummings refuses to take EDI offline. During a mission to destroy stolen nuclear warheads in Tajikistan, Wade realizes that the fallout will cause significant civilian casualties. The human pilots abort, but EDI defies orders and destroys the warheads, causing extensive radioactive fallout and the anticipated casualties. After EDI refuses to return to base, an agitated Gannon decides to shoot it down. In the ensuing dogfight, a missile Purcell fires at EDI explodes on a mountain, blinding him and causing a fatal crash. Wade's plane is damaged by the same explosion, which triggers her plane's self-destruct, and in turn forces her to eject over North Korea. Command realizes EDI is executing a 20-year-old war scenario called 'Caviar Sweep' that involves attacking Russia. Gannon chases EDI into Russian territory where they destroy several Russian Su-37s. After both planes are damaged, Gannon calls a truce with EDI to avoid falling into enemy hands and rescue Wade. Cummings instructs the two to land in Alaska. At risk of facing court-martial for ignoring EDI's behavior, Cummings seeks to eliminate witnesses. He ignores Wade, who heads to the Korean Demilitarized Zone – while evading the army. Cummings orders Gannon eliminated, and orders Dr. Keith Orbit, EDI's creator, to Alaska to wipe EDI's memory. At the Alaskan base, suspecting Cummings' treachery, Gannon narrowly escapes an assassination attempt by the base's doctor and kills him in self defense. Meanwhile, while Orbit inspects EDI, the AI expresses regret for its transgressions. Realizing EDI has developed sentience, Orbit disregards Cumming's order to erase its memory. Orbit reinstalls EDI and Gannon climbs in the same plane as his was damaged during landing. Gannon uses EDI's weapons systems to clear a path for Orbit to flee, then flies to North Korea. Gannon contacts the Lincoln ' s skipper, Captain Dick Marshfield, to inform him about Cummings' deceit. Before Marshfield can order him arrested and court-martialed, Cummings commits suicide. Gannon finds the injured and embattled Wade nearing the border. He lands and runs to her aid. Out of ammunition and taking damage from an Mi-8 helicopter, EDI sacrifices itself by ramming the helicopter, destroying both. Gannon and Wade cross on foot into South Korea, where they are rescued. After attending Purcell's funeral, Gannon awkwardly expresses his feelings of love to Wade. In a post-credits scene, in the debris-strewn border between North and South Korea, EDI's "brain" is seen turning back on.

Teenage boy Zack lives on a farm in Tellico Plains, Tennessee with his mother Frances, younger sister Alice, stern and pious old stepfather Nathan Crane and unpleasant, dim-witted stepbrother Cyrus. One night Frances sneaks out of the house while Nathan is asleep and has sex with Mike, a farm-hand who lives in a nearby shack. Suddenly a large meteorite crashes onto the property, emitting an eerie glow. The next morning, Alan Forbes, a physician who lives nearby, visits the crash site and examines the meteorite, which is a large sphere with a hard shell from which a noxious liquid oozes out. Before long, the object dissolves into glowing gelatinous liquid that seeps into the soil. Forbes wants to contact the authorities but is dissuaded by Charlie Davidson, a local realtor and head of the chamber of commerce, who worries that the event will discourage the Tennessee Valley Authority (TVA) from building a new reservoir in the area. Forbes' bored wife Esther also manipulates her husband into keeping quiet, worried their house will lose its value. The mysterious liquid soon begins to affect the farm. The water from the well grows cloudy and tastes unpleasant, fruit and vegetables grow invitingly large but are rotten and inedible inside, and the livestock begin to behave violently and show severe signs of infection. Alice is attacked and injured by infected chickens and Cyrus is nearly killed by a horse. Frances begins to have large boils growing on her face that grotesquely alter her features. She becomes mentally unstable, physically harming herself and attacking her own family. Believing the blight affecting his farm to be a punishment from God for his wife's infidelity, Nathan locks her in their bedroom, not allowing Zack to tell the doctor. Zack keeps himself and Alice free from the infection by consuming clean water and food he steals from Forbes' house. Forbes secretly obtains a sample from the Cranes' well and has it analyzed at a nearby lab. The water is found to contain a strange, unknown element that alters its metabolic properties and molecular structure. Carl Willis, a TVA representative who is surveying the local area for the planned reservoir, enters the Cranes' house looking for a glass of water. Helping himself from the kitchen faucet, he has just started drinking when he is attacked and nearly killed by Frances, who has gone insane and is horribly mutating. Worried that Forbes is going to alert the authorities, Davidson and Esther arrive at the Crane farm looking for the doctor but are attacked by infected dogs who have turned feral. Esther is mauled to death and Davidson hides himself in the cellar only to be killed and seemingly devoured by Frances, who had been locked in there by Nathan. As Nathan and Cyrus examine infected cows in the shed, the cows begin to decay, revealing maggots and worms inside. The cows explode, covering Nathan and Cyrus in insects. By now Nathan and Cyrus are also infected and beginning to go insane. A guilt-ridden Forbes enters the house, hoping to rescue Zack and Alice, but he is surprised and murdered by Nathan, who then barricades the door. Cyrus attacks Alice but Zack fights him off, hiding his sister in a closet. Nathan corners Zack and is about to kill his stepson when he is stabbed by Willis, who has just arrived. The ground begins to glow and heave beneath the house, which starts to fall apart. Zack locates his mother just in time to see her mutated corpse liquefy. As Zack prepares to leave, Cyrus attacks him, but Zack knocks him off the balcony, seemingly killing him. Nathan is knocked out by a support beam as he attempts to stop Zack. Willis gets Zack and Alice out of the house before it collapses, and a dying Nathan and Cyrus are both killed by falling debris. Willis drives away from the farm, taking Zack and Alice with him. Some months later, a heavily bandaged Willis lies in a hospital bed, having become infected more slowly because he only drank a small amount of the farm's water. He is watching a news report on how the authorities are promising that the blight from the farm will be eradicated. Later, at a location in the nearby countryside, the ground and trees begin to heave and break apart at night, revealing more of the glowing alien liquid spreading onto the surface. A large amount of the substance appears, suggesting that the hostile mutagenic entity is still alive, by planning to complete its invasion of Earth.

In New York City 's Central Park, people begin committing mass suicide. The event is believed to be caused by a bio-terrorist attack using an airborne neurotoxin. The behavior quickly spreads across the Northeastern United States. High school science teacher Elliot Moore and his wife Alma are persuaded by Elliot's mathematician colleague Julian to accompany him and his daughter Jess on a train out of Philadelphia. During the trip, the group learns Boston and Philadelphia have been affected. The train loses all radio contact and stops at a small town. When Julian learns his wife has left Boston for Princeton, he decides to look for her and entrusts Jess to the Moores. However, Julian arrives to find Princeton has been affected, causing the driver of the car in which he is riding to ram into a tree. Julian survives but commits suicide by slitting his wrist with a glass shard. Elliot, Alma, and Jess hitch a ride with a nurseryman and his wife. The nurseryman hypothesizes that plant life has developed a defense mechanism against humans consisting of an airborne toxin that stimulates neurotransmitters and causes humans to kill themselves. The group is later joined by other survivors coming from various directions, and the small crowd chooses to avoid roads and populated areas. When the larger part of the group is affected by the toxin, Elliot suggests the nurseryman was right and the plants are targeting only large groups of people. He splits their group into smaller pockets and they walk along. The trio ends up with a pair of teenage boys, Josh and Jared, who are later shot and killed by the armed residents of a barricaded house. Elliot, Alma, and Jess wander the countryside and come upon the home of Mrs. Jones, an eccentric and paranoid elderly woman. Jones initially agrees to house the group for the night but is suspicious of them having bad intentions; the next morning, she decides to expel them. In a fury, she leaves the house alone and is affected by the toxin. The shaken Elliot realizes the plants are now targeting individuals. Left with no option when Mrs. Jones strikes her head into several windows, the trio chooses to die and embraces in the yard only to find themselves unaffected by the toxin. The outbreak has abated as quickly as it began. Three months later, Elliot and Alma have adjusted to their new life with Jess as their adopted daughter. Alma learns she is pregnant and surprises Elliot with the news. On television, an expert compares the natural event to a red tide and warns the epidemic may have only been a harbinger of an impending global disaster. In Paris 's Tuileries Gardens, people begin committing mass suicide.

American tourists Jenai and Riley arrive in Iceland and visit several landmarks. Riley has taken his father's Rolleiflex camera and plenty of film. When Jenai questions why he prefers it over a modern digital camera, Riley says he prefers to capture the imperfections of the moment rather than have a computer chip auto-correct all the errors. They visit an old church, and a priest tells them some of its history, calling the pre-Christian times simpler. Jenai reveals that her father is a preacher, though she says his church was not as pretty. After retiring for the night, Jenai seems to wake up in the middle of the night and has trouble falling back asleep. Looking out the window to admire the view, she sees strange flashes of the Northern Lights in the distance. Hours later, Riley wakes Jenai to get breakfast. They are frustrated to find that their lodging is not serving breakfast, then confused when they find no staff. They continue having trouble locating other people once they leave: the streets are empty, the stores have no staff, and nobody answers their calls. They spot a running car, and, not being able to locate the owner, appropriate it. As they discuss the possible reasons why the city has become empty, Jenai repeatedly attempts to contact her family in America to no avail. The power and water remain running, but the live television stations broadcast only test signals. Confused, Riley and Jenai return to the hotel after eating, finding no websites have been updated since yesterday. Riley remains optimistic, and suggests they make the most of the situation. He leads them on a shopping spree, eventually filling up two SUVs with goods from the seemingly abandoned stores. He amuses himself by photographing Jenai at scenic locations and performing stunts. Jenai, however, begins sinking into depression, missing her old life. She is further frustrated when Riley injures himself during a reckless stunt, and she pressures him to promise not to put himself at any further risk. As their supplies grow scarcer, Jenai and Riley are forced to ration. Riley angers Jenai when he eats perishable food out of the agreed-upon order based on expiration date. He says he can simply farm for more food if necessary, but she insists they follow the agreement. Seeing Jenai's poor mood, Riley attempts to cheer her by bringing her to the abandoned husk of an airplane he found. Riley calls it beautiful, but Jenai sees only a reminder of the dead world they now inhabit. After Jenai becomes overwhelmed by the decaying city, Riley suggests they go camping. Exploring a cabin, they come upon an old man named Nils. After they give him food and water, he explains that he left the city early on and returned to his cabin. Initially excited to find another survivor, Riley becomes frustrated with Nils' defeatist attitude. Nils tells Jenai about his home life: as a young man, he left his family for lengthy periods to make money as a fisherman. When he returned, he found they had changed. Jenai is disturbed when he says he did not protest this, as he believes it is useless to fight against God's will, which he says does not take humanity into consideration. The next morning, Riley tells Jenai that Nils has died. Thinking back to his philosophy, she asks why they should even bother burying him. Riley insists on doing it because "it's what we do". After they return to the city, Jenai becomes obsessed with searching for more survivors. Riley suggests she is looking for answers where there are none and that they should instead be trying to make the best of their new life. Jenai excitedly opens an email waiting for her on their laptop but is crushed when it is revealed to be a picture from Riley, who is enthused about taking pictures of Iceland in a new season. Riley, when he returns home, becomes concerned when he finds a package of developed pictures left for him by Jenai. Looking all over for her, he finally finds her body floating in a geothermal pool, having apparently drowned herself. Riley initially attempts suicide but instead drives off, anguished, without burying her.

In 1997, a space shuttle lands at a secret military base where a young man, Billy, steps out and is interrogated by a military superior, Felix. He begins recounting his story. Research is being carried out on possible control of the weather. The technical equipment for this is on board the Florida ARKLAB space station, which is jointly operated by the United States and Europe. There, the two astronauts Max and Billy are researching the possibilities of influencing the climate and weather patterns on Earth with microwaves. Billy enjoys a close relationship with Max for the several months they spend together in isolation. Max's wife, Eva, contacts the ARKLAB to announce that she has decided to divorce him because his time away has strained their relationship. At the same time, there is a coup d'état in Saudi Arabia which Billy is oblivious to but Max is closely watching on the TV. The technology of weather control becomes misused for military purposes. Control of the civilian station is taken over by the American military. When the station flies over Saudi Arabia, the systems are taken over by the ground and some substance is vented outside. Max asks the ground controllers for more info and is rebuffed. It turns out that the effect of the microwave radiation is used as a cloak of invisibility for US forces against satellite-based reconnaissance and is thus intended to conceal a military intervention by the United States in Saudi Arabia from the UN. Max uses Billy's security codes to uncover more classified information. Billy sees a news report that a US military operation to free hostages in Saudi Arabia has succeeded, but does not tell Max. Max knows that the irradiation of the affected regions will most likely lead to severe natural disasters. He goes to manually disable the systems the next time they are supposed to spray radiation, but is injured in the process and the station itself gets damaged. Ground control relieves him of duty. Two other astronauts, Eva and Gregor, are sent up on a Space Shuttle to help repair the reactor and ensure it is meeting its military objective. Gregor is authorized to enforce the orders of the military by force, Eva is supposed to exert influence on Max through her relationship with him. Gregor has the order to carry out another irradiation for military reasons and is put under massive pressure by the military to carry it out. Max tries to stop him and attempts to leak information about the military plot to the European press. Gregor disconnects the wiring just before they are in communications range and seriously wounds Max with gunshots. Max kills him, and confesses his love for Eva before succumbing to his wounds. However, the renewed use of the microwave emitters leads to a core meltdown in the already damaged reactor system. Gregor dies while trying to leave the station. Billy screams Max's name as the station falls apart. He and Eva escape in the shuttle as the station explodes. Back on Earth, Felix then tells him that the monsoon set in early due to the microwave irradiation in India and that gigantic floods have occurred as a result with enormous casualties. Afterwards, Eva and Billy are taken away by soldiers. Shortly afterwards, Felix hears on the news that the two have allegedly died of radiation poisoning they suffered in the disaster at the station. He then destroys the recordings of the interrogation.

On July 21, 1969, a robotic eye emerges from the lunar soil and observes the landing module of the Apollo 11 mission taking off. Twenty years later, the Space Shuttle Camelot encounters a derelict spaceship in orbit around Earth. Mission commander Colonel Jason Grant leaves the Shuttle to investigate. He discovers a reddish-brown pod and a mummified human corpse. Both are brought back to Earth, where it is found that they originated on the Moon some fourteen thousand years ago. Shortly thereafter, the unattended pod comes to life. It constructs a cybernetic body with parts from the lab and pieces of the ancient corpse. The cyborg kills a lab technician and exchanges fire with security guards before Grant destroys it with a shotgun blast to the head. Using the last completed Apollo rocket, Grant and fellow astronaut Ray Tanner go to the Moon on a search-and-destroy mission. They discover the ruins of an ancient human civilization. Inside, they find a woman in suspended animation who identifies herself in a rudimentary fashion as Mera and reveals the name of the killer cyborgs — the Kaalium. They survive a Kaalium attack and return to the Lunar Module, with Mera wearing her own spacesuit, but the module is gone. The Kaalium also shoot down the command module, leaving the astronauts stranded on the Moon. In subsequent attacks by the Kaalium, Tanner is killed while Grant and Mera are taken prisoner. The Kaalium head to Earth in a giant ship with the humans aboard. Grant and Mera free themselves and find the landing module, which has been enmeshed in the ship's machinery. Grant supposes the module was the last piece of equipment that the Kaalium needed to complete their ship. He starts the module's self-destruct sequence before he and Mera exit through a breach in the hull, using his gun's recoil as a propellant. The ship explodes after they have reached safe distance. Some time later, Grant and Mera are shown as a couple living on Earth. Having learned to speak English, Mera explains that she was put in stasis to warn others about the Kaalium. Grant reassures her that the Kaalium have been defeated. Later, a Kaalium pod that survived the explosion is shown in a junkyard preparing to build itself a new body. In a post-credits audio clip, Grant speaks to a NASA official about the possibility of any debris that may have fallen to Earth in the aftermath of the ship's explosion. The official dismisses his concerns and assures Grant that any debris from the alien ship would have burned up in the atmosphere.

Distinguished Professor Gordon explains that Earth is being tormented by periodic "sex rays", which send people into a sexual frenzy. When one of the rays hits the passenger aircraft carrying Flesh Gordon and Dale Ardor, the pilots abandon the controls and everyone aboard has manic sex. Realizing no one is flying the plane, Flesh temporarily snaps out of the effects of the ray and tries to pilot the vehicle, to no avail. Seeing no other solution, he takes a parachute and escapes with Dale from the imminent crash. They land near the workshop of Dr. Flexi Jerkoff, who has a plan to stop the sex rays at their source. They travel to the planet Porno aboard Jerkoff's phallic rocket ship, and are briefly hit by a sex ray, resulting in a frantic three-way orgy. After being shot down by the minions of Emperor Wang, the heroes crash land. They run away from their pursuers and enter a nearby cave, where several one-eyed Penisauruses attack them. Wang's soldiers then shoot down the creatures and imprison the earthlings. They are brought before Wang, who is presiding over a sex orgy of more than a dozen men and women. Jerkoff is sent to work in the palace's laboratory, while Wang announces his intention to marry Dale. Flesh is sentenced to death, but is saved from execution by Queen Amora, who takes him as her sex slave. To achieve this, Amora takes Flesh to her ship, which departs for the stars while she hypnotizes him and they make love. Angry at her rebellious attitude, Wang shoots down Amora's airship, and Flesh is the only survivor. Jerkoff escapes the palace and reunites with Flesh, and they resume their efforts to defeat Emperor Wang. To aid them in their quest, Amora's spirit lends them her "power pasties", which turn out to be powerful weapons against Porno's soldiers. The heroes manage to interrupt Wang and Dale's wedding before it is fully realized, and a fight ensues. During it, Dale is kidnapped by Amazonian lesbians. Their leader, Chief Nellie, attempts to initiate Dale into their warrior sex cult. Flesh and Jerkoff save her, unexpectedly aided by Prince Precious of the Forest Kingdom. With help from their new ally, Jerkoff builds a weapon to destroy the sex ray. During the mission, they confront Wang and trick his "rapist robots" into turning on him. However, Wang escapes, seeking the aid of the towering idol of the Great God Porno. Porno comes to life and captures Dale, doing a running commentary like a jaded hipster as they flee. Shooting the living idol, Jerkoff frees Dale and causes the god to fall on Wang. The crash destroys the sex ray and kills them both. Flesh, Dale, and Jerkoff are celebrated as heroes of the planet Porno, thank Prince Precious (the true heir of planet Porno) and return to Earth.