In 1924, Richard and his father Melville walk through the woods where Melville shows his scientific inspiration for Richard.In 1934, Richard and Arline are in high school and their romantic relationship starts.The story jumps to his college years and Arline getting sick with lymphatic tuberculosis.It continues to his move west to Los Alamos National Laboratory in Los Alamos, New Mexico, where Arline follows him later to a hospital in Albuquerque, New Mexico, where she dies.The film ends with Feynman crying at the sight of the red dress Arline had pointed out.

A scientist in the distant future has set out to avert a catastrophic ecological disaster and sends a small number of high tech devices that resemble toys back in time to the 21st century. Ending up in Seattle, they are discovered by siblings Noah Wilder and his younger sister Emma. The "toys" are initially incomprehensible to them, other than one which appears to be a stuffed rabbit. The children keep their discovery a secret from their parents. Emma becomes telepathically connected to the rabbit, naming it "Mimzy", which imparts knowledge onto her. The children gain genius -level intellects and psionic powers – Noah can teleport objects using a card-sized rectangle of green lines of light and a conch shell to control spiders, but thanks to her link, Emma develops more advanced abilities, becoming the only one who can use the "spinners", stones that can float and produce a force field. Emma describes herself as "the chosen one" but names Noah as "the engineer" without which she cannot "build the bridge to the future". The children's parents and Larry White, Noah's science teacher, discover the devices and the children's powers. By mistake, Noah causes a power outage over half the state of Washington, alerting the FBI to their activities. The family is held for questioning by Agent Nathaniel Broadman, during which Mimzy is revealed as artificial life using nanotechnology created by Intel. Emma relates a dire message from Mimzy which states that many of her kind were sent into the past before, but none of them were able to return to their proper time period, because they lacked an "engineer" like Noah, and now Mimzy, the last one that the scientist was able to send back, is beginning to deteriorate. To save the future, Mimzy must acquire a sample of uncorrupted human DNA to correct the damage done to DNA by ecological catastrophes. The FBI do not believe them, so Noah and Emma use their powers to escape. Mimzy absorbs a tear from Emma, which contains her DNA. Via the time portal that Noah constructs using the toys, Mimzy returns to the future, leaving a Sri Yantra symbol; Larry, who witnessed the event, says he saw "numbers", a reference to a dream he had that related to him winning lottery numbers he had missed out before by never buying a ticket. In the future, Mimzy provides the genetic information required to restore humanity, both physically and mentally, with Emma coming to be dubbed "Our Mother" by the populace.

The film opens to Adam Beckett, a pianist reluctantly performing Chopin to an audience in Carnegie Hall. When Beckett is asked to play an encore, he gives away that he is not actually playing, but using a player piano. The outraged crowd storms the stage and wraps Beckett with the piano rolls. Adam awakens on a train in Europe and realizes it was a nightmare. He is accosted by a Swedish architect, to whom he explains his stymied dreams of becoming an artist. After encouragement from him, Adam resolves to return to America to follow his dream. Upon returning, he discovers that the Port Authority has taken control of New York and is restricting entry into the city. Upon failing a drawing test at the Port Authority, Adam is forced to work in a menial job under a trigger-happy boss. He has to watch traffic before it enters the Holland tunnel and prevent vehicles from entering with faulty parts, such as a headlight out. Feeling he won't be creative living under his aunt and uncle's roof, Adam moves to a hotel. He is given a room whose last occupant disappeared mysteriously, leaving all of his belongings behind, including several paintings. At work Adam meets Mara, a fellow aspiring artist. He tags along with her to SoHo and she takes it upon herself to expose them to lots of different art forms to determine which most appeals to each of them. His kindness to a tramp leads him to be taken into an underground network where he is first cleansed by fire, then discovers that the city's tramps are controlling the destiny of all the cities in the world. They instruct him to travel to the Moon on a mission. When Adam returns above ground he goes immediately to Mara's, but she is indifferent to him. Upset, he hurries to the city bus bound for the Moon. In transit, the bus has different levels, one for dancing, one for dinner. Adam is the youngest by far, and one of the older ladies tells him they all have chips implanted in the back of their necks. It causes them to say Miami rather than Moon when they speak of the trip. Upon arrival the bus is greeted by the Moon Maidens and Eloy, meant to be Adam's true love, who tells him it's too dangerous to talk. Adam jumps off the shuttle heading to the shopping at Moon-o-Rama and Eloy picks him up with a buggy to take him out of Consumerzone. Adam awakens in an alley. He's told he must hurry to his concert in Carnegie Hall. After playing Chopin's polonaise no. 53 he receives a standing ovation. He looks up and sees Eloy waving to him from a box.

In the year 2039, Earth is attacked by an alien civilization from Alpha Centauri. Force field domes are put in place to protect cities, and a totalitarian global military government is established to effect the war and the survival of humans. The Centaurians have never been physically seen. Thirty years later, Spencer Olham, a designer of top-secret government weapons, is arrested while on his way to work by Major Hathaway of the Earth Security Administration (ESA), being identified as a replicant created by the aliens. The ESA intercepted an alien transmission which cryptanalysts decoded as programming Olham's target to be the Chancellor, whom he was scheduled to meet. Such replicants are perfect biological copies of existing humans, complete with transplanted memories, and do not know they are replicants. Each has a powerful "U-bomb" in their chest in the exact design of a human heart, which can only be detected by dissection or a high-tech medical scan, since it only arms itself and detonates when it gets in close proximity to its target. Detection via the special scan works by comparing against a previous scan, if there was one. Major Hathaway begins interrogating Olham. As Hathaway is about to drill out Olham's chest to find the bomb, Olham breaks loose and escapes, accidentally killing his friend Nelson in the process. With the help of underground stalker Cale, Olham avoids capture and sneaks into the hospital where his wife Maya is an administrator to get the high-tech scan redone and prove he is not a replicant. But the scan is interrupted by security forces before it can deliver the answer. That evening, after fleeing from the city, Olham and Maya are eventually captured by Hathaway's troops in a forest near an alien crash site, close to the spot where they spent a romantic weekend just a week or so before Olham's arrest. Inside the ship they discover the corpse of the real Maya, and Hathaway shoots and kills the replicant Maya before she can detonate. Hathaway thinks he has killed the true impostor, but as his men move debris away from the Centauri ship, the real Spencer Olham's body is revealed as well. At that moment, Olham realizes aloud that both Maya and himself really are alien replicants, and the secondary trigger (his awareness of what he truly is) detonates his U-bomb, destroying himself, Hathaway, his troops, and everything else in a wide area in a fiery nuclear explosion. A news announcement states that Hathaway and the Olhams were killed in an alien enemy attack, implying that the government covered up or are unaware of the truth. Cale wonders if he ever really knew Olham's true identity.

In the late 1990s, the National Security Agency (NSA) and a computer software firm, Wendell Crenshaw work together to implement a surveillance technology, the Echelon, which enables NSA to monitor almost anybody in the world. When classified information about the Echelon system accidentally finds its way into a young woman's hands, a terrible clash occurs in the opinions of a top-executive at Wendell Crenshaw and an NSA operative, the former determined to find out what the lady knows even if it means using violence and the latter, equally determined to save an innocent woman's life.

In 1988, 11-year-old Dade "Zero Cool" Murphy is banned from owning or operating computers and telephones until his 18th birthday, after his family is fined US$ 45,000 for his crashing of 1,507 computer systems, causing a 7-point drop in the NYSE. On his 18th birthday, Dade has moved to New York City with his mother, and his ban is lifted. While he hacks into a local TV station, another hacker by the handle of "Acid Burn" counters Dade's attack and eventually kicks him out. At school, Dade joins a group of hackers: Ramon "The Phantom Phreak" Sanchez, Emmanuel "Cereal Killer" Goldstein, Paul "Lord Nikon" Cook, Joey Pardella (a novice hacker without an alias and the youngest member), and Kate "Acid Burn" Libby—the hacker who kicked him out of the TV station earlier. Joey, out to prove his skills, breaks into a "Gibson" supercomputer owned by the Ellingson Mineral Corporation. While he is downloading a garbage file as proof of his feat, his mother disconnects his computer, leaving him with a fragmented file. His intrusion has been noticed and brought to the attention of computer security officer Eugene "The Plague" Belford, a former hacker. Plague realizes that the downloaded garbage file is a worm he himself inserted to defraud Ellingson. Claiming the file is the code to the "Da Vinci" computer virus that will capsize the company's oil tanker fleet, and pretending the hackers are to blame, he enlists the U.S. Secret Service to recover the file. In fact, Plague had inserted the "Da Vinci" virus as a red herring to cover for his worm. Joey is arrested and his computer is searched, but he had hidden the disk containing the file. Dade and Kate make a bet: Dade chooses a date with Kate if he wins, and Kate has Dade be her slave if she does. The hacking duel targets Secret Service Agent Richard Gill, who was involved in Joey's arrest. After various hacks, including canceling Gill's credit cards, fabricating a criminal record, and changing his payroll status to "deceased", the duel remains a tie. Released on bail, Joey reveals the disk to Phreak, who is arrested the next day, and informs Kate that the disk is hidden in a bathroom at school. Dade refuses to help Kate and Cereal Killer as he has a record, but copies the disk so they have untampered evidence. Determining that Dade did not hack into Ellingson, Plague sends him a powerful laptop and asks Dade to join him. He later threatens to have Dade's mother incarcerated with a manufactured criminal record, forcing Dade to deliver a copy of the disk. Kate, Lord Nikon, Cereal Killer, and Dade learn that the code is a worm designed to steal $25 million from Ellingson transactions, and that the Da Vinci virus is set to capsize the oil tanker fleet the next day to provide cover and distract from the worm. Dade confesses that he gave Plague a copy of the disk and reveals his hacking history as "Zero Cool". Dade and Kate seek out Razor and Blade, producers of Hack the Planet, a hacker-themed TV show. Lord Nikon and Cereal Killer learn that warrants for their arrest are to be executed at 9 a.m. the next day. The next morning, Dade, Kate, Nikon, and Cereal roller-blade from Washington Square Park, evading the Secret Service by hacking the traffic lights. Meeting up with Joey at Grand Central Terminal, they use payphones and acoustic couplers to hack the Gibson. At first, their attempts are easily rebuffed by Plague, who calls Dade to taunt him. Razor and Blade have contacted hackers around the world, who lend their support and distract Plague long enough for Joey to download the file. After crashing the Gibson, Dade and company are arrested. Dade cryptically informs Cereal Killer that he has tossed the disk in a trash can. As Dade and Kate are being interrogated, Razor and Blade jam TV signals and broadcast live video of Cereal Killer revealing the plot and Plague's complicity. Plague is arrested by Gill on board a flight while attempting to flee to Japan. Their names cleared, Dade and Kate begin a relationship.

A terrible storm causes hundreds of dikes to break in Zeeland, resulting in the North Sea flood of 1953. Julia, a single mother living with her parents, is caught in the middle of a catastrophic flood. She is rescued from drowning and taken to safety by her neighbor Aldo, who is a member of the armed forces. However, her baby is left in a wooden box in the attic of Julia's parental home. Together Julia and Aldo return to the disaster area to look for the baby. When they finally find the box, it is empty, and they conclude that someone must have taken the child. The child ended up with a woman who recently lost her own baby in a car accident. Julia met her but because the woman did not want to lose the baby, she hid him from Julia. Eighteen years later, Julia meets her son and the woman again and she finds out what has happened.

In 1995 in the Ura Valley, Bhutan, four friends—Greg, Fiona, Ruthie, and Paul—go hiking on a mountain. Paul hears a strange whistling and falls into a crevice. Greg finds him in an almost catatonic state, staring at a massive, ancient humanoid skeleton with inhuman features embedded in the cave wall. Paul warns Greg against touching him, or he will die. Ignoring the warning, Greg carries Paul out. The group takes refuge at an empty house as a snowstorm hits. The next day Ruthie is chased by a tall creature wearing robes, which disappears. That night, the paralyzed Paul whispers something into Ruthie's ear. The following morning, they wake up to find Paul sitting near the bridge they crossed yesterday. As Greg shouts at Paul, a dazed Ruthie stabs Greg and slices Fiona's throat, then pushes them off the cliff. She shares an entranced look with Paul before throwing herself off too. Paul helplessly watches, shedding a single tear. In Missouri 2018, former detective James Lasombra is grieving the deaths of his wife Allison and son Henry in a car crash a year prior. He is friends with his neighbor Nora, a widowed single mother. Nora's daughter Amanda runs away leaving a message in the bathroom that reads "The Empty Man made me do it". Searching her bedroom for clues, James discovers a flier from a group called the Pontifex Institute with the word tulpa written on the back. Amanda's friend Davara reveals that Amanda encouraged them to summon the Empty Man, a local legend. To summon him, one must find an empty bottle on a bridge, blow into it, then think of the Empty Man. The next day, Davara witnesses Amanda whispering into their friend Brandon's ear. James investigates the bridge and finds the empty bottle. He blows on it, goes underneath the bridge, and discovers the hanged bodies of Brandon and the rest of Amanda's friends with the same message found in the bathroom. Davara sees the Empty Man, who kills her with a pair of scissors. A brief flash shows Davara holding herself by the throat and stabbing herself with the scissors. The police rule her death a suicide. James researches the Pontifex Institute, discovering it is a cult that has beliefs originating from places like Bhutan and in tulpas. He believes he hears the Empty Man that night and is besieged by nightmares. He travels to the institute and sits in on a talk by cult leader Arthur Parsons. He is alarmed at the leader's references to the Empty Man, claiming him to be an entity that provides his followers with what they want as long as they do his bidding. James begins to think he sees the Empty Man. He follows cult members and investigates a cabin in the woods where he finds files on Amanda, her friends, Paul, and himself. He witnesses the cult performing a fire ritual but is spotted and pursued. He suspects that Amanda is now a member of the cult and informs Nora that she is not safe. He takes Nora to a hotel to hide. It is revealed that the pair were having an affair and he was with Nora when Allison and Henry died. Suffering from hallucinations, James kidnaps a cult member, Garrett, and asks him what is happening before brutally beating him. Garrett says a man in the hospital is the Empty Man's speaker. The man turns out to be Paul, who is regularly visited by cult members to get messages from the entity. James finds Amanda in Paul's hospital room. James calls Nora, but she does not know who he is. Amanda explains that Paul is dying from the strain of being the Empty Man, and that the cult needs a new vessel. She tells James that he is a tulpa, a new vessel for the being, and that his memories and relationships were fabricated by her and the cult to ensure the deity's connection through his pain and loss. The anger, grief, and fear in his life were key to allowing connection with the Empty Man. According to Amanda, James has only existed for a few days. James breaks down and finds himself in a limbo-like plane, where he is chased and caught with the being entering his body. He experiences flashbacks and distortions that show his memories wavering and distorting out of existence. Back in the hospital, James executes Paul. James finds himself surrounded by members of the hospital staff. They bow to him, now bound by the nameless entity.

In the aftermath of nuclear apocalypse, 99% of the survivors are sex Negatives – they become violently ill if they attempt to have sex. The minority sex Positives are forced to engage in carnal theater for the entertainment of the Negatives at Café Flesh. Everyone is excited about the arrival at the club of the famous Positive Johnny Rico, and one Negative woman is beginning to question her negativeness as she and her husband grow more distant from each other.

Anthropologist Stanley Shephard is brought to an arctic base when explorers discover the body of a prehistoric Neanderthal caveman who has been frozen for 40,000 years. After thawing the body to perform an autopsy, the scientists detect brainwaves on the EEG monitor and proceed to successfully resuscitate the "iceman." The dazed Neanderthal is alarmed by the surgical-masked figures; only Shephard has the presence of mind to remove his mask and reveal his humanity and somewhat familiar (bearded) face, permitting the iceman to settle into a peaceful recuperating sleep. The scientists place the iceman in an artificial, simulated environment for study, though the iceman quickly deduces that he is far from home. Shephard believes that the iceman's culture may provide clues to learning about the human body's adaptability, citing ceremonies such as firewalking. Other scientists see the potential in studying the iceman's DNA and his survival in the ice, for possible "freezing" of the sick until treatment is possible. Shephard defends the iceman's right to be considered a human being and not a scientific specimen. Despite opposition from the others, Shephard initiates an encounter with the iceman. Shephard names him "Charlie" after the iceman introduces himself as "Char-u." Shephard and Charlie bond, but it becomes obvious to the anthropologist that Charlie misses his world. A linguist is brought to the Arctic base, and the scientists make progress communicating with Charlie. Shephard introduces Charlie to Shephard's colleague, Dr. Diane Brady. Assuming that the woman is Shephard's mate, Charlie makes lines in the sand that indicate that he likely was a man with a mate and children before he was frozen. Shephard strives to understand what motivates Charlie and why he survived being frozen. At one point, Shephard begins to sing " Heart of Gold ", inspiring Charlie to sing one of his own songs. Charlie's line drawings in the ground resemble a bird, matching body markings on his chest. When the base's helicopter strays over the roof of Charlie's area, he takes on an obsessive zeal as he climbs toward the roof. Shouting the word Beedha, he lifts his arms toward the helicopter in a sign of worship. Even though the helicopter pulls away from the dome, Shephard knows that Charlie can now think of nothing else. Shephard consults local Inuit who recognize the name that Charlie chanted and explain that it is a mythical bird, a messenger for the gods. Shephard understands that Charlie has a spiritual side and that he was on a dreamwalk pilgrimage, a mythical quest for redemption. His people were dying in the sudden ice age; he must have offered himself to the gods in the form of a self-sacrifice or an appeal to the gods to redeem his tribe. Charlie escapes after watching Shephard exit the biosphere. In a panic of seeing unfamiliar modern devices, and believing they are his enemies, he accidentally spears Maynard, one of the base's technicians, before being recaptured, and Shephard's experiment is put to an end. However, Shephard helps Charlie escape into the wild. Charlie races on ahead of Shephard as they pass by glaciers and ice shelves; a crevasse opens up in front of Shephard, cutting him off from Charlie. When the helicopter emerges over an ice shelf, Shephard looks on helplessly as Charlie grabs hold of one of its landing skis. In an attempt to evade Charlie's grasp, the helicopter pilot pulls up, but Charlie dangles beneath the aircraft while it continues to climb high into the sky. Charlie is ecstatic, believing the "messenger" is taking him to his god. He releases his grip, seeming to float through the sky while he plunges to his death. Shephard's initial horror turns into joy, as he realizes that Charlie has reached his "dreamwalk" goal that he began 40,000 years earlier, even though it means his death.