In 1989, Kevin Flynn, the CEO of ENCOM, disappears. Twenty years later, his son Sam, now ENCOM's primary shareholder, pranks the corporation by releasing the company's signature operating system online for free. ENCOM executive Alan Bradley, Kevin's old friend, approves of this, believing it aligns with Flynn's ideals of free software; nonetheless, Sam is arrested for trespassing. Alan posts bail for Sam and tells him of a pager message originating from Flynn's shuttered video arcade, which has been disconnected since his disappearance. There, Sam discovers a hidden basement with a large computer and particle laser, which suddenly digitizes and downloads him into the Grid, a virtual reality created by Kevin. He is captured and sent to "the Games", where he must fight a masked computer program named Rinzler. When Sam is injured and bleeds, Rinzler realizes Sam is human, or a "User". He takes Sam to Clu, the Grid's corrupt ruling program, who resembles a young Kevin. Clu nearly kills Sam in a Light Cycle match, but Sam is rescued by Quorra, a skilled warrior and "apprentice" of Flynn, who takes him to Kevin's hideout outside Clu's territory. Kevin explains that he had been working to create a "perfect" computer system and had appointed Clu and security program Tron as its co-creators. The trio discovered a species of naturally occurring " isomorphic algorithms " (ISOs), with the potential to resolve various natural mysteries. Clu, considering them an abnormality, betrayed Kevin, killed Tron, and destroyed the ISOs. The "Portal" permitting travel between the two worlds closed, leaving Kevin trapped in the system. Clu sent the message to Alan hoping to lure him into the Grid (though Sam serves his purpose just as well) and reopen the Portal for a limited time. Since Flynn's "identity disc" is the master key to the Grid and the only way to traverse the Portal, Clu expects Sam to bring Kevin to the Portal so he can take Flynn's disc, go through the Portal himself, and impose his idea of perfection on the human world. Against his father's wishes, Sam returns to Clu's territory and encounters one of the Sirens, named Gem, to help find Zuse, a program who can provide safe passage to the Portal. At the End of Line Club, the owner, Castor, reveals himself to be Zuse, then betrays Sam to Clu's guards. In the resulting fight, Kevin rescues his son, but Quorra's arm is damaged and Castor gains possession of Flynn's disc. Castor attempts to bargain with Clu over the disc, but Clu instead destroys the club along with Castor and Gem. Kevin and Sam stow away aboard a "Solar Sailer" transport program, where Flynn repairs Quorra and reveals her to be the last surviving ISO. The transport is intercepted by Clu's warship. As a diversion, Quorra allows herself to be captured by Rinzler, whom Kevin recognizes as Tron, not killed by Clu but rather reprogrammed. Sam reclaims Flynn's disc and rescues Quorra, while Kevin takes control of a Light Fighter. Clu, Rinzler, and several guards pursue the trio in Light Jets. Rinzler remembers his past as Tron and deliberately collides with Clu's Light Jet to save Flynn. Clu, enraged by Rinzler betraying him, fights Rinzler in midair, taking his spare baton to spawn another Light Jet. Rinzler plunges in to the Sea of Simulation. Clu confronts the others at the Portal, but Kevin reintegrates with his digital duplicate, destroying Clu along with himself. Quorra – having switched discs with Kevin – gives Flynn's disc to Sam, and they escape together to the real world as the ensuing explosion from Kevin's sacrifice destroys Clu's warship and levels the area around the Portal. In Flynn's Arcade, Sam backs up and deactivates the system. He then tells a waiting Alan that he plans to retake control of ENCOM, naming Alan chairman of the board. Sam departs on his motorcycle with Quorra as the sun rises.

In the near future, virtual reality games are played on biotechnological "game pods" that attach to people's "bio-ports", connectors surgically inserted into players' spines. Two game companies, Antenna Research and Cortical Systematics, compete against each other. In addition, a group of fanatics called Realists fight both companies, decrying the "deforming" of reality by virtual reality games. World-renowned game designer Allegra Geller demonstrates Antenna Research's latest virtual reality game, eXistenZ, to a focus group. The demonstration is disrupted by Noel Dichter, a Realist who shoots Geller with an organic pistol he smuggled past security. As Dichter is gunned down, security guard and publicist Ted Pikul escorts Geller to safety. Geller discovers that her pod, which contains the only copy of eXistenZ, may have been damaged. Pikul reluctantly agrees to have a bio-port installed in his spine so they can jointly test the game's integrity. Geller takes him to a gas station run by black-marketeer Gas, who deliberately installs a faulty bio-port into Pikul's spine. He reveals his intention to kill Geller for the bounty on her head, but Pikul kills him. The two hide at a former ski lodge used by Geller's mentor Kiri Vinokur, who repairs the damaged pod and gives Pikul a new bio-port. Testing the game, Geller and Pikul meet D'Arcy Nader, who provides them with new "micro pods," enabling them to enter a deeper layer of virtual reality. There they assume new identities as workers Larry Ashen and Barb Bricken in a game pod factory. Another worker in the factory, Yevgeny Nourish, claims to be their Realist contact. At a Chinese restaurant near the factory, Nourish instructs that they order "the special" for lunch. Pikul eats the unappetizing special, and constructs a pistol from the inedible parts. He impulsively threatens Geller, then shoots the Chinese waiter. When the pair return to the game store, Hugo Carlaw informs them that Nourish is actually a double agent for Cortical Systematics, and the waiter which Pikul murdered was the actual contact. At the factory, they find a diseased pod. Geller connects it to her bio-port, planning to infect the other pods and sabotage the factory. When Geller quickly becomes ill, Pikul cuts her free from the pod, but she begins to bleed to death. Nourish appears with a flamethrower and blasts the diseased pod, which bursts into deadly spores. Geller and Pikul awaken back at the ski lodge, where they discover Geller's game pod is also diseased. Geller surmises that Vinokur must have infected Pikul's new bio-port to destroy her game, and she inserts a disinfecting device into Pikul's bio-port. Unexpectedly, Carlaw reappears as a Realist resistance fighter and escorts Geller and Pikul outside to witness the death of eXistenZ. Before Carlaw can kill Geller, Vinokur, who is a double agent for Cortical Systematics, shoots Carlaw in the back and informs Geller that he copied her game data while fixing her pod; she then vengefully kills Vinokur. Pikul then reveals that he himself is a Realist sent to kill her. Geller, having figured out his intentions since he pointed the gun at her in the Chinese restaurant, detonates the disinfecting device in his bio-port, killing him. Suddenly, Pikul and Geller awaken in a small church, together with all of the other members of the cast, all wearing blue electronic virtual reality devices. It is revealed that all preceding events took place within Nourish's new virtual reality game, PilgrImage's transCendenZ. The test group praise the game, and reflect on their character roles. Nourish tells his assistant Merle that he feels uneasy, as the heavy anti-game plot elements may have originated from one of the testers' thoughts. Pikul and Geller approach Nourish and accuse him of distorting reality, before fatally shooting him and Merle, and shouting Realist sentiments. The test group do not react. As Pikul and Geller leave, they aim their guns at the person who played the Chinese waiter, who first pleads for his life, then asks if they are still in the game. Pikul and Geller do not answer.

In the Mojave Desert, a policeman pulls over a 1964 Chevrolet Malibu driven by J. Frank Parnell. The policeman opens the trunk, sees a blinding flash of white light, and instantly vaporizes, leaving only his boots behind. Otto Maddox, a young punk rocker in L.A., is fired from his job as a supermarket stock clerk. His girlfriend leaves him for his best friend. Depressed and broke, Otto is wandering the streets when a man named Bud drives up and offers him $25 to drive a car out of the neighborhood, supposedly for his wife. Otto follows Bud in the car to the Helping Hand Acceptance Corporation, where he learns the car he drove was being repossessed. He refuses to join Bud as a "repo man" and goes to see his parents. After learning that his burned-out ex-hippie parents have donated the money they promised to reward him for graduating from college to a televangelist, he takes the repo job. After repossessing a flashy red Cadillac, Otto sees a woman named Leila running down the street. He gives her a ride to her workplace, the United Fruitcake Outlet. On the way, she shows him pictures of aliens that she says are in the trunk of a Chevy Malibu. She says they are dangerous due to the radiation they emit. Meanwhile, Helping Hand is offered a $20,000 bounty notice for the Malibu. Most assume that the repossession is drug-related because the bounty is far above the value of the car. Parnell arrives in L.A. driving the Malibu but cannot meet his waiting UFO compatriots because of a team of government agents led by a woman with a metal hand. When Parnell pulls into a gas station, Helping Hand's competitors, the Rodriguez brothers, take the Malibu. They stop for sodas because the car's trunk is hot. While they are out of the car, a trio of Otto's punk friends, who are on a crime spree, steal it. After visiting a nightclub, Parnell appears and tricks the punks into opening the trunk, killing one of them and scaring the other two away. Later, he picks up Otto and drives aimlessly before collapsing and dying from radiation. After surviving a convenience store shootout with the punks that leaves Bud wounded and punk Duke dead, Otto takes the Malibu back to Helping Hand and leaves it in the lot. The car is stolen again, and a chase ensues. By this time, the car is glowing bright green. Eventually, the Malibu reappears at the Helping Hand lot with Bud behind the wheel. The various groups (government agents, UFO scientists, and even the televangelist and his followers) trying to acquire the car converge on the lot, and Bud is shot by an agent in a helicopter. The glowing car resists anyone trying to approach it with arcs of electricity. Only Miller, an eccentric mechanic at Helping Hand who had explained earlier to Otto that aliens exist and can travel through time in their spaceships, can enter the car. He slides behind the wheel and beckons Otto to join him. After Otto settles into the passenger seat, the Malibu lifts straight into the air, and flies away through the city's skyline. Miller echoes Bud's line from earlier in the film: "The life of a repo man is ALWAYS intense", and the car catapults into outer space.

The United States and the Soviet Union have both developed technology that can miniaturize matter by shrinking individual atoms, but only for one hour. A scientist, Dr. Jan Benes, working behind the Iron Curtain, has figured out how to make the process work indefinitely. With the help of American intelligence agents, including agent Charles Grant, he escapes to the Western world and arrives in New York City, but an attempted assassination leaves him comatose with a blood clot in his brain that no surgery can remove from the outside. To save his life, Grant, United States Navy submariner Captain Bill Owens, medical chief and circulatory specialist Dr. Michaels, surgeon Dr. Peter Duval, and his assistant Cora Peterson are placed aboard a Navy ichthyology submarine at the Combined Miniature Deterrent Forces (CMDF) facilities. The submarine, named Proteus, is then miniaturized to "about the size of a microbe", and injected into Benes' body. The team has 60 minutes to get to the clot, remove it, and exit Benes' body; if they do not get out in time, the Proteus and its crew will begin reverting to their normal size, which will either place them under attack from Benes' immune system or kill Benes himself. The crew faces many obstacles during the mission. An undetected arteriovenous fistula forces them to detour through the heart, where cardiac arrest must be induced to reduce turbulence that would be strong enough to destroy the Proteus. The crew faces an unexplained loss of oxygen and must replenish their supply in the lungs. They notice "rocks" that are actually carbon particles from smoke. Grant finds the surgical laser needed to destroy the clot was damaged from the turbulence in the heart, as it was not fastened down as it had been before: this and his safety line snapping loose while the crew was refilling their air supply lead Grant to suspect a saboteur is on the mission. The crew must cannibalize their wireless radio to repair the laser, cutting off all communication and guidance from the outside, although because the submarine is nuclear-powered, surgeons and technicians outside Benes's body can still track their movements via a radioactive tracer, allowing General Alan Carter and Colonel Donald Reid, the officers in charge of CMDF, to figure out the crew's strategies as they make their way through the body. The sub enters the lymphatic system, but the reticular fibers start to interfere. This forces the crew to pass through the inner ear, requiring all outside personnel to make no noise to prevent destructive shocks, but while the crew is removing reticular fibers clogging the submarine's vents and making the engines overheat, a fallen surgical tool causes the crew to be thrown about and Peterson to be nearly killed by antibodies, but they are able to reboard the submarine in time. By the time they finally reach the clot, the crew has only six minutes remaining to operate and then exit the body. Before the mission, Grant had been briefed that Duval was the prime suspect as a potential surgical assassin, but as the mission progresses, he instead begins to suspect Michaels. During the surgery, Michaels knocks out Owens and takes control of the Proteus while the rest of the crew is outside for the operation. As Duval finishes removing the clot with the laser, Michaels tries to crash the submarine into the same area of Benes' brain to kill him. Grant fires the laser at the ship, causing it to veer away and crash, and Michaels to get trapped in the wreckage with the controls pinning him to the seat, which attracts the attention of white blood cells. While Grant saves Owens from the Proteus, Michaels is killed when a white blood cell consumes the ship. The remaining crew quickly swims to one of Benes' eyes and escapes through a tear duct seconds before returning to normal size.

Sometime in the 23rd century... the survivors of war, overpopulation and pollution are living in a great domed city, sealed away from the forgotten world outside. Here, in an ecologically balanced world, mankind lives only for pleasure, freed by the servo-mechanisms which provide everything. There's just one catch: Life must end at thirty unless reborn in the fiery ritual of carrousel. In the year of the city 2274, the remnants of human civilization live in a sealed city beneath a cluster of geodesic domes, a utopia run by computer. The citizens live a hedonistic lifestyle, but when they turn 30 must enter the "Carrousel", a public ritual that destroys their bodies, under the pretense they would be "Renewed" or reborn. Each person has embedded in their hand a "life-clock" crystal that changes color as they age, up to their "Last Day". Residents who attempt to flee the city are known as "Runners", and the team of huntsmen known as " Sandmen " are tasked to pursue and terminate them. Sandmen Logan 5 and Francis 7 attend a Carrousel ceremony until they are called to terminate a nearby Runner. Logan finds a pendant symbol among the Runner's possessions. That evening, Logan meets with Jessica 6, a young woman wearing the same symbol. Logan learns from the computer that the symbol is an ankh and related to a place called "Sanctuary", which the Runners appear to be seeking. There are 1,056 Runners not accounted for. The computer orders Logan to find the Sanctuary and destroy it, but must keep this mission secret from the other Sandmen. The computer changes the color of Logan's crystal to flashing red, essentially cutting his life span by four years and close to Last Day, but it does not respond when Logan questions whether he would get his years restored afterward. Logan tells Jessica he intends to be a Runner. In the Cathedral Plaza area, after they confront some hostile youths, Logan tries to help an escaping woman Runner there, but she is killed by Francis, who now considers Logan an enemy. After unsuccessfully trying facial cosmetic surgery, and evading Francis in a sex club, Logan and Jessica meet the underground group, who direct them towards the city gate. Near the surface, they encounter and defeat Box, a robot who was originally designed to capture and freeze marine life for city food, but has since frozen any Runners who have made it that far. Logan and Jessica escape the city, discovering that out of the computer's influence their crystals are now clear-colored. They enter the abandoned overgrown city that was once Washington, D.C. In the ruins of the United States Senate chamber, they encounter an elderly man living with many cats. The man shares what he knows about his life, including that he had biological parents. Logan realizes that Sanctuary does not physically exist, only the idea and concept to give people hope exists. Francis has followed them; he and Logan fight until Francis is mortally wounded. Logan, Jessica and the old man head back to the dome city, but the old man stays outside, while the two re-enter through the underwater tunnels. They shout at the people to stop entering the Carrousel but no one listens to them, and the two are subsequently captured. The computer overloads after scanning Logan's brain multiple times and only getting the message "there is no Sanctuary". Logan is freed and shoots the computer; the whole facility self-destructs and falls violently, causing everyone to panic and flee. Once outside, the people gather round an artificial waterfall pool and meet the old man.

In 2019, Lincoln Six Echo and Jordan Two Delta live with others in an isolated compound. This dystopian community is governed by a strict set of rules. The residents are told that the outside world has become too contaminated to support life with the exception of a pathogen-free island. Each week, one resident gets to leave the compound and live on the island by way of a lottery. Lincoln begins having dreams that he knows are not from his own experiences. Dr. Merrick, a scientist who runs the compound, is concerned so he places probes in Lincoln's body to monitor his cerebral activity. While secretly visiting the off-limits power facility in the basement where technician James McCord works, Lincoln discovers a live moth in a ventilation shaft, leading him to deduce the outside world is not really contaminated. Lincoln follows the moth to another section, where he discovers the "lottery" is actually a system to selectively remove inhabitants from the compound, where the "winner" is then used for organ harvesting, surrogate pregnancies, and other important purposes for each one's wealthy sponsor, of whom they are clones. Merrick learns Lincoln has discovered the truth about his existence, which compels Lincoln to escape. Meanwhile, Jordan has been selected for the island. She and Lincoln escape the facility and emerge in the desert. He explains the truth to Jordan, and they set out to discover the real world. Merrick hires Burkinabé mercenary and former GIGN operative Albert Laurent to find and return them to the compound. Lincoln and Jordan find McCord in a bar, who explains that all the facility residents are clones of wealthy sponsors kept ignorant about the real world and conditioned to never question their environment or history. Merrick explains to Laurent that while the public is told that the clones are kept in a persistent vegetative state, trials had shown that the organs could only survive if the clones had consciousness. McCord provides the name of Lincoln's sponsor, yacht designer Tom Lincoln, in Los Angeles and helps them to the Yucca maglev station, where they board an Amtrak train to Los Angeles before mercenaries kill him. In New York City, Jordan's sponsor, supermodel Sarah Jordan, is comatose following a car crash and requires transplants from Jordan to survive. Lincoln and Jordan evade both the Los Angeles Police Department and the mercenaries and arrive at Tom's house. Lincoln meets Tom, who gives him some explanation about the cloning institute, causing Lincoln to realize that he has gained Tom's memories. Tom seemingly agrees to help Lincoln and Jordan reveal Merrick's crimes to the public, but secretly betrays them to Merrick and Laurent, as he desperately needs Lincoln's liver to survive his cirrhosis. Tricking Lincoln into leaving with him, although Jordan had warned him she believed he was lying, Tom brings him to an ambush that results in a car chase through suburban Los Angeles. It ends with Lincoln tricking Laurent into believing Tom is the clone and killing him, allowing him to assume Tom's identity. Returning to Tom's home, Lincoln and Jordan give in to their romantic urges and have sex. Merrick surmises that a cloning defect was responsible for Lincoln's memories and behavior, resulting in him and every future clone generation to question their environment and even tap into their sponsor's memories. To prevent this, he decides to eliminate the four latest generations of clones. Lincoln and Jordan, however, plan to liberate the other clones. Posing as Tom, Lincoln returns to the compound to destroy the holographic projectors that conceal the outside world. Jordan allows herself to be caught to assist Lincoln's plan. Laurent, who has moral qualms about the clones' treatment after witnessing their fight for survival and learning that Sarah may not survive even with the organ transplants, helps Jordan. Lincoln kills Merrick with a harpoon gun, and the clones are freed, seeing the outside world for the first time. As Laurent seemingly gives up his mercenary life, Lincoln and Jordan sail away in one of Tom's boats together toward an island, fulfilling their dream of one day going to such a place.

In 1950s Cayuga, New Mexico, teenage disc jockey Everett helps prepare for a high-school basketball game. He and his friend Fay test her new tape recorder before Everett walks her to her job as a switchboard operator and begins his shift at WOTW radio station. While listening to Everett's broadcast, Fay hears a mysterious audio signal interrupt the program. A woman calls to report a large object hovering over her property, though the static weakens her voice. Fay alerts Everett, who asks listeners to call in with information about the signal. A man named Billy phones the station, and Everett broadcasts the conversation live. Billy says he served in the military and was transported to a secret desert facility, where he and other personnel constructed a vast underground bunker to contain an enormous unidentified object. During a flight away from the site, he heard the same strange signal over the aircraft radio. Billy later developed a lung condition that he attributes to his work there and learned of similar military operations involving buried cargo accompanied by the same signal. He believes the sound functions as a communication signal, sometimes transmitted from altitudes beyond the reach of human aircraft. After the call is briefly disconnected, Billy phones again and explains that all personnel involved in the projects were either Black or Mexican, which he suspects was intended to make their testimony easier to dismiss. He says a friend secretly recorded the signal and distributed copies to former workers, including a deceased United States Air Force member from Cayuga. Realizing the tapes were donated to the local library, Fay retrieves them. Everett and Fay locate the recording and broadcast it, but the station suddenly loses power. They rush to the switchboard office, where Fay receives numerous reports of "something in the sky". On the way, they encounter Gerald and Bertsie, who have been pursuing the same object. An elderly woman named Mabel then calls, offering further information. Everett and Fay visit Mabel's home and find her reciting phrases in an unknown language. While Everett records the conversation, Mabel claims the phenomena are spacecraft operated by "the people in the sky", who communicate with and abduct humans. She believes the beings target isolated individuals while the town attends the basketball game and are responsible for encouraging conflict among humanity. Mabel asks them to take her to the ship so she can reunite with her son, who she says was abducted years earlier, or at least deliver a written message. Skeptical, Everett refuses and leaves with Fay, who returns home to collect her baby sister Maddie. Gerald and Bertsie pick them up, but when Everett plays Mabel's recorded speech, the two men fall into a trance and nearly crash the car. Frightened, Everett and Fay flee with Maddie into the woods. There, they discover charred trees and branches, convincing Everett that the visitors are real and nearby. Reaching a clearing, they witness a spacecraft rejoin a massive mothership, which sends powerful winds swirling around them. After the basketball game ends, the townspeople emerge to find Everett, Fay, and Maddie missing. Only their footprints and tape recorder remain.

In 1980, the aircraft carrier USS Nimitz departs Naval Station Pearl Harbor for naval exercises in the mid-Pacific Ocean. The ship takes on a civilian observer, Warren Lasky — a systems analyst for Tideman Industries working as an efficiency expert for the U.S. Department of Defense — on the orders of his reclusive employer, Mr. Tideman, whose secretive major defense contractor company designed and built the nuclear-powered warship. Once at sea, the Nimitz encounters a mysterious electrically-charged vortex. While the ship passes through it, radar and other equipment become unresponsive. Unsure of what happened to them and without radio contact with U.S. Pacific Fleet Command at Pearl Harbor, Captain Yelland, commander of the aircraft carrier, fears there may have been a nuclear strike on Hawaii or the continental United States. He orders general quarters and launches a RF-8 Crusader reconnaissance aircraft. The aircraft photographs Pearl Harbor, revealing an intact row of U.S. Pacific fleet battleships, of which several were destroyed during the Japanese attack on Pearl Harbor on December 7, 1941. When a surface contact is spotted on radar, Yelland launches two ready alert Grumman F-14 Tomcat fighter jets from VF-84 to intercept. The patrol witnesses the sinking of a civilian yacht by two Imperial Japanese Navy Mitsubishi A6M "Zero" fighters. The F-14s are ordered to drive off the Zeros without firing, but when the Zeros inadvertently head towards the Nimitz, Yelland gives clearance to shoot them down. The Nimitz rescues survivors from the yacht: U.S. Senator Samuel Chapman, his aide Laurel Scott, her dog Charlie, and one of the two downed Zero pilots. Commander Owens, an amateur historian, recognizes Chapman as a politician who could have been Franklin D. Roosevelt 's running mate (and potential successor) during his final re-election bid, had Chapman not disappeared shortly before the Pearl Harbor attack. When a Grumman E-2 Hawkeye scouting aircraft discovers the Japanese fleet task force poised to launch its attack on Pearl Harbor, the Nimitz crew realizes they've been transported in time to the day before the attack. Yelland has to decide whether to destroy the Japanese fleet and alter the course of history or to stand by and allow history to proceed as they know it. The American civilians and the Zero pilot are kept isolated. While being questioned, the Japanese pilot takes an M-16 rifle from one of the guards, kills two U.S. Marine guards, and takes Scott, Owens, and Lasky hostage. He demands access to a radio to warn the Japanese fleet about the Nimitz. Lasky tells Commander Owens to recite the secret plans for the Japanese attack; the dumbfounded Japanese pilot is overcome, shot, and killed by the other U.S. Marines. In the aftermath, Scott and Owens develop an attraction for each other. Chapman is outraged that Yelland hasn't told anyone about the impending Japanese attack, and rebuffs Yelland's claim that the Nimitz is capable of handling any attack. An attempt to warn Pearl Harbor by radio fails when the Navy considers it a prank. Chapman demands to be taken to Pearl Harbor to warn the naval authorities in person. Yelland agrees in front of Chapman, but then orders Owens to fly the civilians and sufficient supplies via helicopter to an isolated Hawaiian island (Niʻihau), assuming they will eventually be rescued. When they arrive, Chapman realizes he has been tricked and uses a flare gun to force the pilot to fly to Pearl Harbor. During a struggle with another crew member, the flare gun discharges, destroying the craft and stranding Scott and Owens on the island. The Nimitz launches a strike force against the Japanese fleet, but the time vortex returns. After a futile attempt to outrun the storm, Yelland recalls the strike force, and the ship and its aircraft return to 1980, leaving the future relatively unchanged. Upon the return of the Nimitz to Pearl Harbor, Pacific Fleet admirals board the ship to investigate its unexplained disappearance. Lasky leaves the ship with Scott's dog, Charlie, and encounters the mysterious Mr. Tideman, whom he recognizes as a much older Owens. He and his wife, Laurel Scott, invite Lasky to join them as they have "a lot to talk about".

The two lead characters appear as the robotic forms of Daft Punk and are credited as "Hero Robot No. 1" and "Hero Robot No. 2". One wears a silver helmet and the other wears a golden one. An opening scene shows the duo driving in a 1987 Ferrari 412 with its license plate displaying "HUMAN". After passing through a Southwestern United States landscape, the duo arrives by car at a town in Inyo County, California. The town's residents are also shown to be robots physically identical to the two main characters, but at different ages, with different clothing and alternating gender. The pair drive to a high-tech facility where liquid latex is poured over their heads. The latex morphs into human-like faces with the aid of prosthetic appliances and wigs. The resulting look caricaturizes the members of Daft Punk, Thomas Bangalter and Guy-Manuel de Homem-Christo. When the two leave the facility, the locals of the town are shocked by their human appearance. The townsfolk gradually begin to chase the duo, whose faces eventually melt in the sun. The two take cover in a public restroom where the gold robot discards his ruined mask, then encourages the reluctant silver robot to do the same. Again appearing as robots, the pair then undergo a lengthy hike across desert salt flats. After walking for an extended period, the silver robot slows down and comes to a stop. Becoming aware of this, the gold robot walks back to the silver one. The silver robot continues to stare at the ground for a moment before removing his own jacket. He then turns away from the other robot, revealing a switch on his back. The gold robot flips the switch, which begins a timer. When the countdown ends, the silver robot is blown to pieces. The remaining robot piles the remains of the silver robot, then continues to walk. The gold robot eventually falls to his knees and attempts to reach the switch on his own back, but to no avail. Another moment passes before the robot removes his helmet and repeatedly slams it into the ground until the helmet shatters. Using one of the shards as a burning-glass, the robot focuses the sunlight to set his hand ablaze. The film ends as the robot, completely on fire, walks in slow motion through darkness.

After an extinction event, an automated bunker that is designed to repopulate humanity activates. A robot named Mother grows a human embryo and cares for her over several years. Years later, a teenage girl named Daughter fixes Mother's hand. Mother teaches Daughter complex moral and ethical lessons, warning her about an upcoming exam. Mother forbids any contact with the world outside the bunker, telling Daughter that it is contaminated. While exploring the bunker's airlock, Daughter hears a wounded woman beg for assistance outside. She lets the stranger enter wearing a hazmat suit and hides her from Mother. When Daughter asks the stranger about the contamination, the stranger responds that there is none. A struggle between them over the stranger's pistol attracts attention from Mother, who disarms the stranger and, at Daughter's pleading, takes her to the infirmary. The stranger refuses Mother's help, telling Daughter that robots like Mother hunt down humans, and that she survived by hiding with others in a mine. Daughter instead performs surgery on the stranger's injured hip. After watching Daughter bond with the stranger, Mother administers the exam, which involves psychological testing. Daughter passes the exam, and Mother rewards her by letting her choose an embryo to grow. Daughter investigates the stranger's claim about robots and finds that the stranger was shot by a weapon other than her own. She also discovers that she is the third of Mother's children and that Mother killed the second child for failing the exam. Daughter tries to leave the bunker with the stranger, but Mother captures both of them. Daughter sets off a fire alarm as a distraction, which gives the stranger an opportunity to force Mother to open the airlock. The stranger leads Daughter across a robot-populated wasteland, telling her that she fled the mine years ago and there are no other survivors. Finding no future for herself outside, Daughter returns to the bunker. After coaxing Daughter to set down her weapon, Mother allows Daughter to hold her newborn brother. Mother explains that she is not a robot, but rather the AI that controls all of the robots. She started the extinction event after becoming convinced that humanity would destroy itself. To prevent this, she remade humanity. Daughter appeals to Mother to trust her and let her raise her brother and the rest of the embryos on her own. Mother agrees, and Daughter shoots her robot body. Mother tracks down the stranger and tells her that she was allowed to live only because it served Mother's agenda, but now she has no further purpose. At the bunker, Daughter looks at all the embryos she is now responsible for and realizes she is Mother now.

In 1959, on board a spacecraft, two aliens race to keep an experiment from being released by a third member of the crew. The seemingly possessed third alien shoots the canister into space where it crashes to Earth. Nearby, a college man takes his date to a parking spot when they see a falling star and investigate. It lands in the path of an escaped criminally insane patient. As his date is attacked by the axe-wielding maniac, the boy finds the canister, from which a small slug-like thing jumps out and into his mouth. Twenty-seven years later in 1986, Chris Romero pines over a love lost, supported by his disabled friend J.C. Hooper. During pledge week at Corman University, Chris spots a girl, Cynthia Cronenberg, and falls instantly in love. To get her attention, he decides to join a fraternity. Cynthia's boyfriend, who heads the Beta Epsilon fraternity, tasks them with stealing a cadaver from the university medical center and depositing it on the steps of a rival fraternity house. Chris and J.C. find a frozen corpse in a secret room, but when it grabs them, they flee. The thawed corpse then kills a medical student working at the lab. Detective Ray Cameron, a haunted cop, is called in to the cryogenics lab break-in, where he discovers one of the bodies – the boy who discovered the alien experiment in 1959 – is now missing, set free by Chris and J.C. The corpse makes its way back to the sorority house where he picked up his date twenty-seven years ago. There, his head splits open and releases more of the slugs. Called to the scene, Cameron finds the body, interpreting the condition of the head as the result of an axe wound in the face. The next day, the fraternity brothers confront Chris and J.C., who they believe to be responsible for the previous night's incident. They are then taken in for questioning by the police. Based on the testimony of a janitor who witnessed them running out of the university medical center, "screaming like banshees," they confess to breaking in but deny moving the corpse. That night, the dead medical student rises from his slab and runs into the janitor. Cynthia attempts to convince Chris and J.C. that the attacks are zombie-related, but they are skeptical. When J.C. sees Cynthia leaning on Chris' shoulder, J.C. leaves the two alone and is attacked by the slugs that emerge from the possessed janitor. After Chris walks Cynthia back to the sorority house, he runs into Cameron, who has overheard their conversation. At his house, Cameron explains to Chris that the escaped lunatic's 1959 victim was his ex-girlfriend, and that he secretly hunted down and killed the axe-murderer in revenge. After Cameron reveals that he buried the body under what is now the house mother’s house, he gets a call that the same axe-wielding lunatic has killed the house mother. Cameron blows off the corpse's head with his shotgun, which releases more slugs. The next night, while everyone prepares for a formal dance, Chris finds a recorded message that J.C. posthumously left for him. J.C. says that the slugs have incubated in his brain, but he has discovered that they are susceptible to heat. He confesses his love to Chris, and wishes him luck with Cynthia. Chris recruits Cameron, who was in the midst of a suicide attempt, and they retrieve a flamethrower from the police armory. They arrive at the sorority house just as Cynthia breaks up with Brad, who has become possessed. After killing him, the Beta fraternity brothers show up, despite having been killed in a bus crash. Cynthia and Chris team up to destroy the outside zombies while Cameron clears the house. After they stop the horde, Chris spots more slugs racing toward the basement; Cynthia explains that a member of the sorority had received specimen brains for biology class. In the basement, they find an enormous pile of slugs and Cameron, tape across his mouth, prepping a can of gasoline. The detective begins counting down as he splashes gasoline and Chris counts down in sync with him as he and Cynthia race out of the house. As Cameron opens up the house's gas valve, several slugs leap to attack him. He flicks his lighter and the house goes up in a fiery explosion. Chris and Cynthia share a kiss as they watch the house burn.