In a secret military laboratory operating under the guise of a pesticide manufacturer, a sealed tube is broken, starting an outbreak of a virulent bacteria. Detecting the release of the biological weapon, Joanie Morse, the plant's security officer, activates "Protocol One," a procedure sealing all of the workers inside from the outside world. Tom Schmidt, believing the cause for the lock down to be a pump malfunction, and co-worker Bob restart the pump. Cal Morse, a County Sheriff and Joanie's husband, is advised to retain the help of Dr. Dan Fairchild, a past employee who is a known alcoholic. Fairchild created an antidote to the weapon. Vic Flint, Bob's father, joins the mission. The United States government's Accident Containment Team (USACT), led by Major Connelly, arrives and sets up quarantine procedures. Connelly tells the public a cover story of the contamination of experimental yeast while a rescue team arrives to administer the antidote to the workers. Upon the release of the weapon, workers sanitize the lab, destroy animals, and inoculate themselves with the antidote. Hours later, the USACT team locate Dr. Nielsen and his team incapacitated on the floor near an air lock. They later notice that the bodies have disappeared, the air lock smashed open from inside, and a power outage caused by Dr. Ramesh Kapoor, a P4 worker, by destroying a power box. A group of workers—including Bob, Schmidt, and Tippett—believe themselves to be unaffected and want to leave, despite the quarantine. Unbeknownst to the workers, they became infected by the breach of the air lock, the bypassed pump circulating contaminated air throughout the building, and Schmidt's contact lens contaminating the building with the weapon. Joanie destroyed the piece of paper containing the code to deactivate the lockdown, but remembers the code. The group, now led by Tippett, torture her for the code, which is discovered to be invalidated once USACT tapped into the system. The rescue team eventually encounters this group of workers. The team order the group to remain under quarantine; Tippett is killed when he refuses. The rest are placed in a room to await inoculation when the team returns with the antidote. Fairchild directs the team into an unoccupied service conduit as a direct way to the P4 lab. The team encounters Nielsen. Suspecting something to be wrong, Fairchild directs the team to retreat, leaving Nielsen behind. The team are ambushed and murdered by the P4 workers, one of which is murdered by Kapoor. Despite being inoculated, the antidote did not work; suffering from the effects of the weapon, all of the infected workers become homicidal maniacs. Upon the rescue team's death, USACT activates "Protocol Two", leaving all employees to await the deadly effects of the weapon and sanitize the location afterwards. Hearing this, Cal urges Fairchild to assist him in retrieving the antidote, stopping the contagion, and saving Joanie. At the facility, Cal and Fairchild encounter an infected Bob. He tries to attack, but is killed by Cal, armed with the revolver. Most of the workers succumb to their infections, but Joanie is unaffected. Schmidt convinces her to go to the P4 lab to retrieve the antidote. En route, they encounter Nielsen, who wants to contain the knowledge of the incident, and Kapoor, who wants to kill them. They eventually escape the attack. While in the P4 lab, Schmidt succumbs to his infection while the P4 workers hunt them down. Joanie retrieves the antidote and flees while Schmidt attacks the workers, breaking Kapoor's neck before being killed by the rest. Joanie eventually encounters Cal and Fairchild. They later repel a group of workers who rip Fairchild's biohazard suit, exposing him. They enter the P4 lab to learn why Joanie is unaffected while the antidote did not work. A test discovers that her blood is full of estrogen, progesterone, and antibodies; she is pregnant. While attempting to enter P4 to attack the trio, workers are set on fire by booby traps. One worker rips Cal's biohazard suit before being killed by Joanie. Before being incapacitated by his infection, Fairchild enters a recipe for a new antidote based on Joanie's condition into a computer; it contains thorazine to make the patient sleep during their recuperation. They try out the new antidote on Fairchild, and it works. Armed with injection guns, Cal and Fairchild inoculate infected workers while Joanie takes a batch of the new antidote to the building's decontamination system. Nielsen, refusing to be injected, flees back to the lab. Eventually realizing his failure, he commits suicide. Using the decontamination system, Joanie administers the new antidote throughout the building, eradicating the weapon and treating workers breathing in the aerosolized antidote. Joanie then deactivates the quarantine and Fairchild inoculates Cal. USACT then evacuates the victims, retrieves the dead and seals the building.

Dr. John Mathewson discovers a new process for refining plutonium to purities greater than 99.997 percent. The United States government provides him a laboratory located in Ithaca, New York, masked as a medical company. John moves to Ithaca and meets real estate agent Elizabeth Stephens while searching for an apartment. He attempts to win the affections of the single mother by inviting her teenage son Paul to take a tour of the lab. John is confident in the lab's cover story but Paul, an unusually gifted student with a passion for science, becomes suspicious when he discovers a statistically impossible patch of five-leaf clover on the grounds. Paul and his aspiring journalist girlfriend, Jenny Anderman, decide to expose the weapons factory to the media, stealing a container of plutonium as evidence. Once they succeed, Paul declares that the plutonium alone is insufficient, as no-one would be impressed by two kids stealing something from a lab. Instead, he convinces Jenny he can create the world's first privately built nuclear device, exposing the lab to the world by audaciously entering it into the New York Science Fair. After convincing his mother and his school that his project is about hamsters bred in darkness, he begins research and construction of the bomb. The lab discovers that a container of plutonium has been replaced by a bottle of shampoo mixed with glitter. A military investigation team, led by Lt. Colonel Conroy, arrives on the scene and determines that Paul is responsible for stealing the plutonium. Suspecting him of terrorist intent, the investigators search Paul's home and discover that he and Jenny have left for the science fair. After the agents capture the couple in New York City, John, who feels personally responsible for the crisis, talks privately with Paul and persuades him to give the bomb to the agents before a group of other participants at the science fair help Paul and Jenny escape from the hotel. In an effort to expose the lab, Paul hatches a plan to return the bomb on his own terms. Ensuring Jenny is a safe distance away, he calls the agents from a pay phone and walks into the lab with the bomb while being surrounded by snipers and agents. During the standoff, negotiations stall and Paul arms the bomb. John, convinced that Paul is not an actual terrorist, attempts to intercede on his behalf. Due to radiation from the plutonium, the bomb's timer activates on its own and begins to count down with increasing speed. Paul suggests taking the bomb to a quarry outside of town, but John admits that he had not fully understood the ramifications of his plutonium refining process. As a result, Paul's bomb will have a nuclear blast yield nearly five times larger than the one that destroyed Hiroshima if it detonates. Desperate to defuse the bomb, all sides put down their weapons and frantically work as a team to dismantle it. They manage to disarm the bomb a fraction of a second before it explodes. After a brief moment of relief, Conroy decides to arrest Paul. John refuses to cooperate and opens the door to the lab, revealing a large crowd, including Jenny and the press. The film ends with Paul freely departing the scene.

In Evans City, Pennsylvania, a man kills his wife and burns down his farmhouse. Firefighters David and Clank—both Vietnam War veterans—are called to the scene. David's pregnant girlfriend, a nurse named Judy, is called to the office of Dr. Brookmyre, where the two children of the arsonist are being treated for burns. Heavily armed U.S. troops led by Major Ryder take over Dr. Brookmyre's office. Days earlier, an Army plane carrying a bioweapon had crash-landed near the town, infecting the water supply with a virus code-named "Trixie," which is highly contagious and causes victims to either die or become hysterical and homicidally insane. Government officials send Colonel Peckem and Dr. Watts, who worked on the creation of the virus, to Evans City to contain the virus and work towards a cure. Martial law is declared in Evans City and a quarantine is placed on the town. Army soldiers forcibly move the townspeople into a high school, rousting many from their homes, and shoot anyone attempting to escape. Bombers armed with nuclear weapons are dispatched to destroy the town if necessary. David, Judy, Clank, teenager Kathy Fulton, and her father Artie try to find a way to escape the town. After spending the night hiding in a country club, the group attempts to escape through the nearby woods, eluding soldiers both on the ground and in an overhead helicopter. They overpower several soldiers in a house. One of the soldiers discloses what he knows about the virus to David, but when one of the soldiers reaches for his gun, Clank opens fire and kills the soldiers. David tells Judy about what he knows about the virus and that Kathy, Artie, and probably Clank are infected. After Clank beats him for attempting to have sex with Kathy, Artie hangs himself. Kathy wanders outside and is killed by soldiers. Realizing he is infected, Clank kills several soldiers to give David and Judy time to escape. He is then shot and killed. The next night, Judy, now visibly infected, is killed by armed civilians. Angry and frightened, David surrenders to the military. After being taken into custody, David eventually realizes that he is immune to the virus, but he keeps the knowledge to himself. Dr. Watts develops a potential cure for the virus but when he tries to take samples to Peckem and Ryder, he is killed and the samples are destroyed in a stampede of infected townspeople breaking free from quarantine. Depressed and distraught by his experiences in Evans City, Colonel Peckem is ordered to relocate to Louisville, where symptoms of the virus have been reported.

"Cutters" edit the collected memories of the recently deceased into feature-length memorials that are viewed by loved ones at funerals. The "cutters code" forbids them to mix footage from implants, to sell memories, and to have the implant themselves. Ten-year-old Alan Hakman, while visiting a city with his parents, meets another boy, Louis, and the two bond as they play together. Louis reluctantly joins Hakman in exploring an abandoned factory, and Hakman crosses a wooden plank suspended high above the ground. Goaded by Hakman, Louis also attempts to cross the plank, but he loses his confidence and falls. Hakman races to the ground and panics when he steps in what he thinks is Louis's blood. Hakman flees the scene and tells no one what has happened. Later that day, he leaves the city with his parents. Years later, the adult Hakman has become a skilled cutter who specializes in editing the memories of controversial people into flattering life stories. When Fletcher, a former cutter, confronts him at a funeral, Hakman describes himself as a sin-eater, who brings redemption to the immoral. Fletcher offers him $500,000 for the memories of his latest client, wealthy businessman Charles Bannister, but Hakman refuses. In a meeting, Fletcher demands the memory recordings so that he can use Bannister, who he suspects was a pedophile, as a scandal to shut down EYE Tech, the implant manufacturer. Hakman again refuses and, worried for his safety, uses his knowledge from memory tapes to shake down a shady criminal for a pistol. As Hakman works through Bannister's memories, he encounters a scene that implies that Bannister was molesting his daughter Isabel, and Hakman wordlessly deletes it. He eventually comes across a person who he is convinced must be his childhood friend Louis. Excited, he sets up a meeting with Bannister's family to find out more information. Bannister's wife Jennifer is dismissive, but Isabel reveals that the man, recently dead of a car crash, was a teacher named Louis Hunt. Hoping that Hunt had an implant, Hakman organizes a break-in at EYE Tech, but they have no record of Hunt. However, Hakman surprisingly finds a file on himself that contains documentation of his parents' purchase of an implant for him. In his distress, Hakman turns to his lover, Delila. At his apartment, he shows her the equipment that he uses to view memories, and he demonstrates surreal footage from a defective implant. He leaves her alone as he seeks help from anti-implant protestors, who have discovered a way to block the implant through specialized body modification. When he returns to find his apartment in disarray, he assumes that Fletcher has broken in; instead, Delila confronts him, having found memory tapes that document her prior relationship. She accuses him of voyeurism and angrily destroys his memory viewer, which results in Bannister's files also being damaged. Fletcher and his associate finally break in, but they find nothing. Hakman tells Bannister's wife that the erased footage was lost in an accident, and she feigns disappointment, content to let dirty secrets stay hidden. Hakman asks his colleagues to recover live footage from his own implant, a potentially deadly process. They agree but admonish him that he can never cut memories again; a cutter with an implant is a violation of the "Cutter's code". The recorded memories show that Hakman had attempted to dissuade Louis from crossing the plank, and that he had stepped in red paint, not blood. Hakman, relieved, visits Hunt's grave but is confronted again by Fletcher, who has learned about Hakman's implant. After chasing Hakman through the graveyard, he hesitates and seems willing to let Hakman go; however, Fletcher's associate kills Hakman. Fletcher loads Hakman's memories (which contain the memories of everyone he had viewed as a cutter) into a viewer and promises to use them for the greater good. As he pages through Hakman's memories, looking for evidence of Bannister's guilt, he sees the young Hakman looking in a mirror.

Athena-1, a space station owned by nefarious gene-manipulation company Energyne, is destroyed after a laboratory rat mutates and wreaks havoc. Kerry Atkins, the lone surviving crew member, manages to escape in the escape pod when the station implodes, along with a trio of pathogen canisters that Energyne CEO Claire Wyden ordered her to retrieve, but the pod disintegrates upon re-entry, killing Atkins. One canister is swallowed by an American crocodile in the Everglades National Park and another lands in a Wyoming forest where a wolf is exposed to the pathogen. Primatologist Davis Okoye, a former Special Forces soldier and member of an anti-poaching unit, works at the San Diego Zoo Safari Park. He is friends with George, a rare leucistic western lowland gorilla that he rescued from poachers who murdered his mother and communicates with him via sign language. The third Energyne canister crash-lands in George's habitat, exposing him to the pathogen. As George grows considerably larger and more aggressive, Davis is contacted by genetic engineer Doctor Kate Caldwell, who explains that the pathogen was developed by Energyne to rewrite genes on a massive scale. She had hoped to advance research on CRISPR as a potential cure for diseases, but discovered Energyne's plans to use it as a biological weapon and was falsely incarcerated, during which her terminally ill brother died. George escapes from captivity and runs amok at the preserve. George calms down, but is soon captured by a government team led by Agent Harvey Russell and put on a Boeing C-17 Globemaster III airplane. Meanwhile, Claire and her brother Brett oversee a mercenary team's attempt to capture the mutated wolf, Ralph, which goes awry as the entire team is killed. Claire, resolving to capture Ralph and use George to cover up her plot, uses a massive transmitter atop the Willis Tower to lure the animals – engineered to respond aggressively to a certain radio frequency – to Chicago, unconcerned about the massive risk to civilian lives this poses. George reacts violently to the sound and crashes the plane, though Davis, Kate and Harvey parachute to safety. George survives the crash and joins Ralph as they make their way to Chicago, while Davis and Kate are aided by Harvey in stealing a UH-60 Black Hawk military helicopter in pursuit. They arrive to find George and Ralph tearing through the city as the military struggles to stop them. The crisis worsens when the mutated crocodile, Lizzie, joins the duo. Planning to steal an antidote to turn the animals back to normal, Davis and Kate infiltrate Energyne's base of operations at the tower and take several vials of it, but are caught by the Wydens as Claire reveals that the antidote only eliminates the animals' enhanced aggressiveness rather than reversing the pathogen's effects altogether and shoots Davis, but he survives. When George climbs to the top of the tower, Claire orders Davis to distract him while she attempts to escape with Kate at gunpoint. Kate slips a vial into Claire's handbag and pushes her toward George, who swallows her whole along with the vial, returning him to his former personality. Down below, Harvey takes incriminating evidence from Brett and allows him to escape, only for Brett to be crushed to death by falling debris upon exiting the building. As the damaged tower topples, Davis and Kate survive by crash-landing a helicopter on the Federal Plaza. Davis stays to help George defeat the other animals, while Kate and Harvey rush to prevent the military from deploying a GBU-43/B MOAB against them. During their confrontation, Davis tricks Ralph into attacking Lizzie, who decapitates him before gaining the upper hand against her enemies, only to be stabbed to death in the eye by a rebar -wielding George. With the threat neutralized, the airstrike is aborted as Davis is joined by his allies in rescuing misplaced civilians.

At a sleepy gas station, the pump attendant is attacked by an animal infected by an unknown organism manifesting as large protruding splinters. A young couple, Seth Belzer and Polly Watt, drive for a romantic camping trip in the forests of Oklahoma, but are car-jacked by an escaped convict, Dennis Farell, and his drug-addict girlfriend, Lacey Belisle. The group gets a flat tire when they run over a splinter-infected animal on the road. They find shelter at the now-abandoned gas station. Lacey discovers the horribly-infected pump attendant, writhing in the bathroom. She is attacked and killed by the monster, but her corpse slowly reanimates and becomes a new creature, which attacks the remaining survivors. While fighting her, Seth, Polly and Dennis discover that severed pieces of the infected victims are capable of attacking on their own. Sheriff Terri Frankel arrives and attempts to arrest Dennis, but is ripped in half by Lacey's corpse. The creature takes the top half of the officer's body and bonds with it, becoming a larger creature. The trio hide in the walk-in refrigerator when a piece of the creature's arm attacks them. It is discovered that Dennis has been infected, as his left arm violently twists on its own. Seth and Polly amputate his arm to prevent the infection from spreading. Dennis explains that he had been pricked by a splinter from the dead creature they encountered on the road. Seth discovers that the creatures themselves are a fungus taking control of the corpses they infect and consuming the blood in the body, using the currently zombified host to seek out fresh and new hosts. Because of this, they hunt based on temperature and attack the warmest thing they can find. By lowering his body temperature with bags of ice, Seth sneaks past the creature to the police car, while Polly and Dennis distract it with fireworks. Seth discovers that, without the keys, the car and the police radio inside are useless. His body temperature rises again, forcing Dennis to leave the gas station to lure the creature away from him. The creature enters the gas station, and Dennis and Polly hide in the freezer. The discarded fireworks ignite a trail of flammable liquid, and the gas station catches on fire. Seth retrieves a shotgun from the police car and helps Polly and Dennis escape. Dennis is infected after helping to keep the creature at bay while Seth and Polly escape. He shoots one of the gas pumps with the shotgun, and the creature is engulfed in flames, killing it. Dennis, still infected, gives Seth and Polly a key to a bank account, telling them to give it to the wife of a man he shot, who later died. Dennis shoots directly into the propane tanks, incinerating himself, the station, and any remaining infected corpses. Seth and Polly wander into the distance as other infected creature corpses lie dormant in the woods.

A spacecraft presumed to be of alien origin is discovered on the floor of the Pacific Ocean, estimated to have been there for nearly 300 years. A team of experts, including marine biologist Dr. Beth Halperin, mathematician Dr. Harry Adams, astrophysicist Dr. Ted Fielding, psychologist Dr. Norman Goodman and U.S. Navy Captain Harold Barnes, is assembled and taken to the Habitat, a state-of-the-art underwater living environment located near the spacecraft. Examining the spacecraft, the team is perplexed to learn it is not alien at all but rather American in origin. However, its technology far surpasses any in the present day. The ship's computer logs cryptically suggest a mission that originated either in the distant past or future but the team deduces that the long-dead crew was tasked with collecting an item of scientific importance. Norman and Beth discover the ship's logs, with the last entry noting an "unknown event". A holographic reenactment of the event reveals that hundreds of years in the future, the ship encountered a black hole, which apparently led to a crash landing in the ocean, back in the 1700s. Soon after, Norman and the others stumble on a large, yet perfect sphere hovering in the cargo bay. They cannot find any way to probe the inside of the sphere, as the fluid surface seems to be impenetrable. On observation, Norman ominously notes that the sphere reflects everything in the room, except them. When they return to the Habitat, Harry hypothesizes that everyone on this team is fated to die. Harry notes that the black hole is referred to as an "unknown event" in the future logs. However, here in the present, they have knowledge of the historic event, yet it is unable to be explained later on. During the night, Harry returns to the spacecraft and is able to enter the sphere. Norman follows Harry, where he finds him unconscious next to the sphere, and returns him to the Habitat. The next day, the crew discovers a series of numerically encoded messages appearing on the computer screens. The crew is able to decipher them, and comes to believe they are speaking to "Jerry", an alien intelligence from the sphere. They find that Jerry is able to see and hear everything that happens on the Habitat. A powerful typhoon strikes the surface and the Habitat crew is forced to stay in the Habitat several more days. During that time, a series of tragedies strikes the crew, including attacks from aggressive jellyfish and a giant squid and equipment failures in the base that kill Ted, Barnes and the team's support staff. The survivors, Beth, Harry and Norman, believe Jerry is responsible. Norman discovers that they had misinterpreted the initial messages from Jerry, and that the entity speaking to them through the computers is actually Harry himself, transmitted from his mind while he is asleep. Norman and Beth eventually realize that when Harry entered the sphere, he gained the ability to make anything he imagines a reality, and they conclude that all the horrors that have befallen the Habitat were manifestations of Harry's fears. Norman and Beth sedate Harry with enough sleeping drugs to put him into a dreamless sleep to prevent him from doing any further damage. However, when Norman is attacked by a snake, Beth realizes that Harry alone could not have been responsible for everything that had happened on the Habitat and she confronts Norman, accusing him of entering the sphere when he went to retrieve Harry. Beth's suspicions prove to be correct but after experiencing her own nightmarish vision, she confesses to Norman that she too entered the sphere. When rejoined by Harry, the group realizes that the crew of the ship must have also entered the sphere and they ended up killing each other after being driven mad by their fears. Under the stress of the situation, Beth has suicidal thoughts, which causes the detonation mechanisms on a store of explosives to engage, threatening to destroy the base and the spacecraft. They race to the Habitat's mini-sub but their combined fears cause them to reappear back in the spacecraft. As a psychologist, Norman is able to see through the illusion. He triggers the mini-sub's undocking process and overrides the others' fears that they will not escape the destruction of the Habitat and spacecraft. The sphere is untouched by the explosions. The mini-sub makes it to the surface as the surface ships return. As Beth, Harry and Norman begin safe decompression, they realize that they will be debriefed and their newfound powers discovered. Fearing humans are not ready for this ability they agree to erase their memories of the event using their powers, to ensure the "unknown event" paradox is resolved. The sphere then rises from the ocean and accelerates away into distant space.

In the near future, humanity lives in a technologically advanced, dystopian society. The government requires that everyone receive an ocular implant that records everything they see. The implant provides an augmented-reality head-up display to the user with information about anyone and anything they may see, as well as recording the user's view. Investigations into crimes amount to detectives reviewing video and assessing whether an alleged perpetrator is innocent or guilty. Sal Friedland, a detective with the metropolitan police force, crosses paths with a young woman who appears to trigger a glitch in his ocular implant, as no data about her is retrieved. When he reviews his own record of that day, he finds that every single frame of her has been mysteriously deleted. At work, Sal is handed several homicide cases where the victims' own visual records of their deaths are replaced with the killer's point of view, thus hiding the killer's identity. At another murder scene, Sal chases the apparent killer only to nearly be killed when they hack his implant and change what he sees in real time. It is discovered that all the victims hired someone with the expertise to delete pieces of their visual records that were either humiliating or incriminating. The detectives determine that the unknown woman Sal encountered earlier has the ability to manipulate the system in this way, making her their primary suspect. Sal goes undercover, creating a false history as a stockbroker who engages in a brief affair with a prostitute. Using this as the pretext for her services, he makes contact with the woman —who uses the handle 'Anon'— and asks to have his encounter with the prostitute deleted. With his team on standby in the adjacent apartment, the initial plan to apprehend Anon fails when she successfully covers her tracks. Sal and Anon develop a personal relationship. She discovers Sal's true identity and flees, apparently killing one of Sal's colleagues in the process. Anon begins to harass Sal for his betrayal, tormenting him with his worst memories, deleting his memories of his dead son, and causing further hallucinations. His superiors confront him after his neighbor turns up dead with a bullet from Sal's gun in him rejecting his explanation and order him off the case. Despite being under house arrest, Sal tracks Anon to her apartment and tells her that she is being investigated for multiple murders. She reveals that she already knows this and that she is being framed by another hacker with a similar skillset. Anon shows Sal her video record of the second sting operation, in which his colleague was killed, seeming to prove that she is innocent. After showing Sal her records, she flees again. Believing Sal has become too personally involved, his superiors suspend him from active duty. The actual killer attempts to murder him in his apartment, revealing himself to be Cyrus Frear, one of the technical experts from the police department. Cyrus has been obsessed with Anon for years killing anyone who had sex with her out of jealousy and erased every trace of her, even peoples' memories. During a physical altercation between Cyrus and Anon, Sal draws his weapon, but realizes that Cyrus is seeing what he sees in real-time. To defeat this advantage, Sal fires blindly towards Cyrus, successfully killing him. Anon leaves, later revealing to Sal that she is able to bypass the vast surveillance network by disseminating her records in microsecond slices throughout everyone else in the network, rendering her untraceable. When Sal asks her why she is so desperate to hide her identity, she tells him that her quest for anonymity is not because she has something to hide, but merely because she does not want to share herself with the world.

Dr. Larry Roberts, a renowned Beverly Hills plastic surgeon, performs cosmetic procedures on a clientele mainly consisting of female television models. Lisa Convey, one of his patients, falls into a trance state in her apartment after being exposed to a flash of light, unaware of the presence of a man lurking in her closet. She falls from her balcony moments later in what is suspected by police to be a suicide. Lieutenant Masters questions Roberts at his office, where his secretary finds that several medical records—including Lisa's—have mysteriously vanished. After Masters departs, patient Cindy Fairmont visits for a final follow-up appointment, followed by Tina Cassidy. A disturbed Tina begs Roberts to return her to her original appearance, claiming that the "perfect" models in the city are being murdered. As Tina departs, she leaves behind her purse, which contains a document from Digital Matrix Inc. (DMI). When Roberts attempts to return the purse to Tina, he sees a flash of light in her apartment window, and she too falls to her death. Roberts sees a man on her balcony, but he disappears. Fearing for Cindy's safety, Roberts invites her to join him for a fundraising dinner held by billionaire businessman John Reston, who introduces Roberts to the head of DMI, Jennifer Long. She explains that DMI used women's facial measurements for a visual technology experiment that was recently ended. Roberts then brings Cindy back to his residence and, despite her expectation of a romantic encounter, has her sleep in the guest room. The next day, Roberts accompanies Cindy to the filming of a television commercial where DMI technicians monitor the set using a computer. When Cindy is unable to hit her marks, the DMI technicians inform her that the commercial will be completed using CGI which will require Cindy to visit DMI. As Cindy undergoes a 3D body scan at the DMI laboratory, Jennifer tests Roberts' eyes with the computer. His point of focus is shown to be on the model rather than the products advertised. Jennifer divulges that, after surgery, Cindy and other models were assessed as visually "perfect" by the computer in still photos, but their scores were inconsistent while in motion. Roberts notices flashes of light from the "Looker" lab which Jennifer claims her security card will not allow them to enter. Roberts steals a security card from a technician before departing with Cindy and the theft is reported to Reston. While Cindy is visiting her parents, Roberts is exposed to a series of light flashes by the man from Tina's balcony after which hours pass without his awareness. When Cindy returns that night, the two drive to DMI and enter using the security card to breach the Looker lab. Roberts learns that Looker stands for "light ocular-oriented kinetic emotive responses" which uses high-intensity light to induce trances in those exposed. A man enters the Looker lab and attacks Roberts using the Looker gun. Roberts defends himself by using a pair of mirrored sunglasses to reflect the light, immobilizing the assailant. Later, Reston orders the man to abduct Cindy and murder Roberts. Arriving at Roberts's office, they kidnap Cindy. The next morning, Roberts is chased through the city by Reston's henchman, causing Roberts to crash his car, but he escapes. Roberts stows aboard a Reston Industries security car to infiltrate the company headquarters. Onstage for a gala demonstration, Reston introduces his company's newfound ability to create commercials using computer-generated actors. The audience is then mesmerized by Jennifer who is operating the computer from the room where she is holding Cindy. When Jennifer leaves the console, Reston's henchman kills her having mistaken her for Roberts. A struggle between Roberts and the henchman is ended by Reston shooting at Roberts and accidentally killing his own man. Lieutenant Masters, who has been following Roberts, arrives in time to kill Reston before he can shoot Roberts.

In 2025, ENCOM and Dillinger Systems are in a race to bring digital constructs into reality. ENCOM's CEO Eve Kim and her partner Seth Flores visit a remote station near Skagway, Alaska built decades earlier by Kevin Flynn. Finding Flynn's "permanence code", enabling constructs to exist for more than 29-minute intervals, they transfer a digital orange tree into the real world. Julian Dillinger, the head of Dillinger Systems and grandson of former ENCOM executive Ed Dillinger, introduces his shareholders to Ares, a Master Control Program he describes as the "perfect, expendable soldier". Ares shows signs of self-awareness and notes Julian's indifference to his programs' survival, while Julian's mother, Elisabeth, expresses concern about their constructs' limited lifespans. Julian sends Ares and his unit to attack ENCOM's digital Grid, downloading Eve's personal data in pursuit of the permanence code. Against his programming, Ares tries to save an injured program, but Julian extracts him and disables ENCOM's Grid. Redeployed to the outside world, Ares tracks Eve's jet as she and Seth return to ENCOM with the permanence code. Learning of Julian's cyberattack from their colleague Ajay Singh, Eve flees as Ares and his second-in-command Athena chase her through the city on Light Cycles. Eve hijacks Athena's Light Cycle but is cornered by Ares, and destroys the drive containing the code. Reaching the end of his 29-minute lifespan, Ares recognizes Eve's empathy towards his plight. As Ares and Athena are "derezzed", Julian digitizes Eve onto the Dillinger Grid. Ares reveals the code can be obtained using Eve's identity disc, and Julian is willing to let her die as a result. Lying to Athena that Julian is "indisposed", Ares bargains with Eve, asking to achieve permanence in exchange for her freedom. Suspicious, Athena contacts Julian and, deciding that Ares is malfunctioning, returns with orders to de-rez him. Evading their pursuers, Ares and Eve return to the real world. En route to ENCOM, they reflect on their motivations, as Ares shows further signs of self-awareness and individuality. Eve realizes a copy of the code might be stored in Kevin Flynn's original office, preserved at ENCOM Tower, where they reunite with Seth to upload Ares onto Flynn's original Grid using a particle laser. They are ambushed by Athena, who destroys the laser to trap Ares, but experiences a moment of self-awareness before de-materializing. Ajay and his assistant Erin arrive, joining Seth and Eve in using Athena's own laser to hack the Dillinger Grid. Elisabeth retakes the position of CEO and tries to turn off the particle lasers, but Athena re-materializes and fatally stabs her, to Julian's horror, having interpreted her as an obstacle in his directive to obtain the code "by any means". On Flynn's Grid, Ares encounters a manifestation of Flynn, and they discuss Ares's desire for permanence. Intrigued by Ares's wish to live and to save Eve, Flynn grants him the permanence code and re-materializes him via backdoor at Flynn's Arcade. Athena pilots a Recognizer into the city, capturing Eve while the ENCOM staff breach the Dillinger Grid, but Ares intercepts Athena and her unit. Ajay, Seth, and Erin shut down the Dillinger mainframe, preventing Ares's fellow Dillinger programs from re-materializing, and a wounded Athena permanently de-materializes in Ares's arms. The police raid Dillinger headquarters, but Julian uses the laser to digitize himself. Eve and Ares go their separate ways, as ENCOM uses the permanence code to benefit the world. Ares sends Eve a postcard, traveling the world in search of Flynn's son, Sam, and his companion, Quorra. Eve reconstructs the Skagway facility on top of ENCOM Tower, including the orange tree. Back in the damaged Dillinger Grid, Julian is transformed by an identity disc that belonged to his grandfather's program Sark.

High schooler Sara Dunn has a troubled relationship with her mother, whom she constantly avoids. Essentially homeless, she steals food from her mother's house and sleeps in a sleeping bag outdoors or at friends' homes. Her sleep environment affects her ability to stay awake in class and throughout the day. She is also plagued by surreal nightmares of a dark maze and a shadowy figure with glowing eyes. Needing money, Sara agrees to be a test subject in a sleep study, the intent and goal of which are classified. At first, Sara sleeps well but, after two sessions, her nightmares begin to worsen. She learns that one of the scientists, a young man nicknamed Riff, has been following her outside of the study. The only other woman in the study, Emily, seemingly drops out. Sara has a panic attack when a scientist shows her a picture of the same shadowy figure from the nightmares, and she becomes fed up with the fact none of them will divulge the purpose of the study. The head scientist, Dr. Meyer, disallows the younger scientists using unapproved study methods because of what happened to Sara. Sara eventually passes out from seeing a shadowy figure in a laundromat and is robbed of her phone. Sara confronts Riff, insisting that the study has had a negative impact on her and that she will only continue with it if he reveals the study's purpose. He says that the experiment involves monitoring subjects' dreams using a brain scanning device that converts brainwaves into images. During the next session, Sara and the rest of the experiment volunteers all dream of the same shadowy figure. Riff states that, across the world and throughout history, people have dreamed of a similar figure, which has also haunted him since childhood. As their vitals spike, Sara wakes up in a panic, bleeding from her left eye, and runs away after saying that she knows what the other scientists are doing. Riff pursues her as she runs to a club in search of her friend Zoe but passes out, forcing him to carry her unconscious body. At the lab, the two remaining volunteers continue dreaming of the figure. Becoming semiconscious from sleep paralysis, they see the figure standing at the foot of their beds. It moves around in the waking world. After a scientist goes into the volunteers' room, the figure reaches for him and the volunteers sit up awake with white eyes, causing the monitoring system to shut down. Sara wakes up from a nightmare involving the figure and finds herself in Riff's apartment, where he straps himself to his bed and monitors his own dreams. She sees his dream in which the two of them grow fangs and kiss. Then he has the same dream of the figure while entering sleep paralysis. Sara wakes him before the figure reaches him. Traumatized and exhausted, they have sex, during which Sara sees two shadow figures and passes out again. Riff takes her to a hospital. While waiting for a report of Sara's status, Riff begins to dream of a dark maze and a humanoid figure in the waking world. He then learns that Sara has left her room and wandered out of the hospital. She is sleepwalking and her eyes bleed when Riff tries to wake her. He calls his colleague Anita and urges her to help monitor Sara's dreaming as she sleepwalks through the city. Anita and Riff attach a mobile monitor to Sara's head as she unconsciously leads them to a remote, wooded area. Sara's dream mimics the path she is taking, with shadowy figures manifesting on the monitor, seeming to flank the trio. As they enter a field, the monitor shows Sara approaching a large citadel, before Riff finds a cellphone ringing in the grass. When he answers the call, Sara wakes up screaming. Riff comforts Sara, who identifies the phone as hers, despite the fact that she has never been there before. The phone screen grows static and, though awake, Sara sees shadow figures in the trees. The trio flee, but darkness swallows Anita and Riff as a shadow figure approaches Sara. Sara then wakes up again in Riff's apartment, naked and straddling Riff's dead body, having apparently gouged out his eyes in a sleepwalking episode. She goes to the bathroom and receives a text message that makes her laugh. She examines her reflection, discovering that she has fangs, like in Riff's dream. The message says that she has been in a coma for twenty years, she is being studied using a new technique, and the scientists are not sure where in her dream the message will reach her. It begs her to wake up.

A group of wealthy industrialists gather at the home of Mr. Lloyd, a millionaire who introduces them to Richard "Mack" McAllan, the engineer who successfully spearheaded the construction of the Channel Tunnel (the story takes place in the unspecified near-future, though it is noted in the film that the Channel Tunnel is built "in 1940") and so is the Bahamas-Miami tunnel. McAllan informs the group that the "Allanite steel" he developed, along with a "radium drill" developed by his friend Frederick "Robbie" Robbins, makes it possible to construct an undersea tunnel linking England with the United States. Though the group is initially skeptical, the backing of Lloyd and his associate Mostyn convinces the group to buy shares in the project. Three years into construction of the tunnel, McAllan is a worldwide celebrity, but his work keeps him from his devoted wife Ruth and their young son Geoffrey. Called away to New York, he is informed that the people are losing faith in the project. Lloyd needs to have him use his fame to get support. Lloyd's attractive daughter Varlia, who is secretly in love with McAllan, keeps him company to intensify the attention of the press. The photos of the couple add to Ruth's sense of isolation, and she decides to work in the tunnel as a nurse. There she is affected by an unknown gas afflicting the workers and loses her eyesight. Worried that her husband no longer loves her and not wanting him to stay with her out of pity, Ruth leaves McAllan, taking their son with her. Heartbroken at her unexplained departure, McAllan throws himself into the project, alienating Robbins in the process. Years pass. Though the cost of the tunnel in lives and money continues to mount, the British prime minister and American president eagerly anticipate its completion and the unity and peace they promise it will bring. Ruth lives in the countryside with her now-grown son, who lobbies Robbins to find him a job working in the tunnel. The tunnel is nearing completion, but the workers encounter a submarine volcano that will necessitate a detour. McAllan needs more money to establish a detour, but is opposed by Grellier, an arms manufacturer, and Mostyn. The two men earlier manipulated the stock market to become the controlling shareholders in the company. Lloyd suspects that Grellier and Mostyn plan to use the delay to depress stock prices again, and this time gain total ownership of the tunnel. However, Varlia convinces Mostyn to fund further construction by promising him the one thing he has always wanted, but never gotten: her hand in marriage. Though the project goes forward, Grellier has Mostyn killed for backing out of their deal. Despite the renewed effort, samples indicate the volcano may be too large to drill around. The drill breaks through to volcanic gases that kill hundreds of workers, including Geoffrey. The project seems on the verge of collapse. Determined to see the project through and fortified by the reappearance of Ruth (who came to the tunnel site to discover Geoffrey's fate), McAllan vows to continue. With three volunteers, McAllan and Robbins man the radium drill, and despite near-fatal temperatures, break through to the American side of the tunnel.