In August 2005, inside a small, dimly-lit cell, Dalton Russell proclaims he has committed the perfect bank robbery. Some time prior, in New York City, masked robbers, dressed in painter coveralls and using variants of the name "Steve" as aliases, seize control of a Manhattan bank, taking patrons and employees hostage. They divide the hostages into groups and hold them in different rooms, forcing them to don masks and coveralls identical to their own, rotating them among various rooms and occasionally inserting themselves covertly into the groups. They also take turns demolishing and building a replacement fake wall in one of the bank's storage rooms. Police surround the bank, and Detectives Keith Frazier and Bill Mitchell take charge of negotiations. Russell, the head robber, demands food be provided. The police send pizzas whose boxes have hidden listening devices. The bugs pick up someone speaking Albanian (initially misunderstood to be Russian), which is later identified as propaganda recordings of the late Albanian leader Enver Hoxha, implying that the robbers anticipated the attempted surveillance. When Arthur Case, the bank's founder and chairman, learns about the holdup, he hires fixer Madeleine White to try to protect the contents of a safe deposit box within the bank. Russell breaks into a safe deposit box and finds, among other things, documents from Nazi Germany. White, using her influence with the Mayor of New York, is introduced to Frazier and persuades him to let her talk to Russell, who agrees to allow her inside the bank so they can talk privately. Russell implies that Case started his bank with money he received for collaborating with the Nazis, resulting in many Jews dying during World War II. Frazier demands to inspect the hostages before allowing the robbers to leave and Russell shows him around the bank. As he is being shown out, Frazier attacks Russell, but is restrained by another robber. Afterwards, Frazier explains he deliberately provoked him, concluding that Russell is not a killer. However, Frazier's conclusion is almost immediately tested when a hostage execution is staged. The execution prompts an Emergency Services Unit team into action. They plan to storm the bank, using rubber bullets to knock out those inside. Frazier discovers that the robbers have planted a listening device on the police; aware of the police plans, the robbers detonate smoke grenades and exit the bank hidden among the hostages. The police detain and question everyone but cannot distinguish the identically dressed hostages from the robbers. A search of the bank reveals the robbers' weapons were plastic replicas. They find props showing that the hostage execution was faked, and no money or valuables appear to have been stolen. Unable to identify the suspects and unable to show a robbery has even been committed, Frazier's superior orders him to drop the case. Frazier, however, searches bank records and finds that safe deposit box No. 392 has never appeared on any records since the bank's founding in 1948. He obtains a search warrant to open it. White then confronts Frazier to persuade him to drop his investigation and during their conversation she hints at Case's Nazi dealings. Frazier refuses to stop his investigation and plays a recording he had surreptitiously made of an incriminating conversation that took place earlier between White and Frazier and the mayor. White confronts Case, who admits the box contained loose diamonds and a Cartier diamond ring he took from a Jewish friend whom he betrayed to the Nazis. Russell's opening monologue is revealed to have happened while he hid behind a fake wall the robbers had constructed inside the bank's supply room. He emerges a week after the robbery with the contents of Case's safe deposit box, including incriminating documents and several bags of diamonds. On his way out, he bumps into Frazier, who does not recognize him. Russell exits the bank and enters a waiting car filled with his conspirators, some of whom the police had questioned. When Frazier opens the safe deposit box, he finds the ring and a note from Russell that says, "follow the ring". He confronts White, urging her to contact the Office of War Crimes Issues at the State Department about Case's war crimes. At home, Frazier finds a loose diamond and realizes that Russell slipped it into his pocket during their collision while exiting the bank.

In 1985, a man living in a Manhattan apartment watches news about escalating Cold War tensions and the response from five-term President Richard Nixon when an unknown assailant attacks and hurls him to the street below. Throughout the opening credits, a montage reviews the rise of costumed crime-fighters from 1939 to 1977, culminating in public backlash and the passage of an anti-vigilante act. Rorschach, a vigilante detective who operates illegally, discovers that the dead man was Edward Blake, better known as "the Comedian ", a costumed hero who worked for the government. Suspecting that other vigilantes could be attacked, Rorschach warns members of his former team, the Watchmen. Rorschach's former partner Dan Dreiberg believes he is paranoid, but relays his concerns to Adrian Veidt, a crime-fighter turned businessman, but he also dismisses the concerns. Rorschach later visits Doctor Manhattan, a physicist whose accidental superpowers make him a national security asset, but Manhattan is preoccupied with energy research and ignores him. At Blake's funeral, Manhattan, Veidt and Dreiberg each recall the Comedian's pessimism in his later years about the Watchmen's mission. After the service, a lone mourner pays his respects. Rorschach tracks down and questions the mourner, former supervillain Edgar Jacobi. Jacobi says that Blake had recently broken into his apartment while he was sleeping — tearful, unmasked, and incoherent. Rorschach is astonished but doubts that Jacobi would tell a lie so bizarre. During a press interview with Doctor Manhattan, an investigative journalist tells him that several people who had been in contact with Manhattan have developed cancer, including his former girlfriend. As other reporters mob Manhattan with questions, he snaps and exiles himself to Mars. Alone, Manhattan reflects on his existence and his regrets at allowing himself to be turned into a weapon. In his absence, the Warsaw Pact countries make aggressive moves, and Nixon prepares for war. Veidt survives an assassination attempt, suggesting that Rorschach's "mask-killer" theory is correct. Dreiberg takes in Laurie Jupiter, a second-generation vigilante and estranged lover of Manhattan, to whom Dreiberg is attracted. Rorschach's investigation of the assassin leads him back to Jacobi. Rorschach finds Jacobi dead and himself framed for Jacobi's murder. After a battle with police, Rorschach is arrested and unmasked as a low-born vagrant. In prison, Rorschach defends his vigilantism to a psychiatrist, saying he cannot ignore evil and the people who cause it. Dreiberg and Jupiter, after donning their costumes and saving multiple people from a burning building, have sex. Imprisoned crime boss Big Figure stages a riot as a cover for assassinating Rorschach. The attack fails, and Rorschach kills Big Figure and his accomplices before leaving the prison with Dreiberg and Jupiter who have arrived to break him out. Manhattan teleports Jupiter to Mars while Dreiberg joins Rorschach's investigation of the Blake murder. Evidence points them to Veidt as the mastermind; they find him at an Antarctic hideout, where he has just overseen the activation of Doctor Manhattan's energy reactors in New York City and other locations across the planet. On Mars, Jupiter tries to convince Manhattan that humanity is worth saving. She succeeds only when he learns that Jupiter is Blake's illegitimate daughter, a fact so unlikely (as Blake had once tried to rape Jupiter's mother) that it restores his respect for life. Veidt admits orchestrating Manhattan's exile, staging the assassination, framing Rorschach, and killing Blake, who was spying on his activities. He has also executed the final step of his plan: turning the world against Manhattan by rigging his reactors to explode, killing 15 million people. Manhattan returns with Jupiter to a devastated New York, pieces together what has happened, and teleports to Veidt's hideout. After a brief struggle, Veidt shows him that the world's countries have put aside their rivalries to focus on a common enemy: Doctor Manhattan. Realizing the logic of Veidt's plan, the Watchmen agree to keep his secret, except for Rorschach, whom Manhattan reluctantly kills to preserve the new global peace. Manhattan departs permanently for another galaxy while Dreiberg rebukes Veidt's moral sacrifice, and Jupiter finally comes to terms with her parentage. A New York tabloid editor, disgusted that there is no war to report on, tells a staff member to choose something from the "crank file", which contains Rorschach's journal.

David Kim lives in San Jose, California with his daughter, Margot. His wife, Pamela, was diagnosed with lymphoma and died before Margot entered high school. David calls Margot who says she is with a study group and will be there all night. That same night, Margot attempts to call David three times, but he is asleep. The following day, David is unable to contact Margot. Believing she is attending her piano lesson, David calls the instructor, but is told that Margot canceled her lessons six months earlier. He finds a phone for her friend Isaac and finds out from Isaac's mom that he and some friends, including Margot, are on a camping trip in the mountains. Once Isaac reaches out to him he finds out that Margot never made it on the trip with her friends prompting him to call and file a missing person's report. The case is assigned to Detective Rosemary Vick. Through her social media accounts, and after speaking with "friends" of Margot David learns she isn't really close with any of the friends and Margot has become a loner since Pamela's death. He discovers she pocketed and transferred $2,500 to a now-deleted Venmo account. Vick reports Margot made a fake ID and shows traffic camera footage of her car outside the city, suggesting she may have run away. Unconvinced, David discovers Margot had been using a streaming site called YouCast, and befriended a young woman named Hannah. Vick reports Hannah's innocence, having been sighted in Pittsburgh at the time of the disappearance. From Margot's Tumblr account, David notices she frequently visited Barbosa Lake near the highway where she was last seen. He finds her Pokémon keychain there, and the police discover her car in the lake, which contains an envelope with $2,500. A search party is organized, but a storm delays the operation. After David has an altercation with a boy who claims to know Margot's whereabouts, Vick tells him he can no longer participate in the investigation. Undeterred, David visits TMZ, which displays the crime scene photographs, and notices his brother Peter's jacket. He discovers text messages between Margot and Peter that suggest an incestuous relationship. Upon confrontation, Peter explains they were only smoking marijuana and confiding in each other. He chastises David for being negligent towards Margot, who is still grieving Pamela's death. Vick calls David and tells him an ex-convict named Randy Cartoff confessed to raping and killing Margot before committing suicide. An empty-casket funeral is arranged for Margot. As David uploads photos to a funeral streaming site, he notices the website's stock photograph features a picture of Hannah. Discovering she is a stock model, he contacts her, and she reveals that she does not know Margot and that the police never called her. Talking to a police dispatcher, David learns that Vick was not assigned to the case but volunteered. He discovers she knew Cartoff through a volunteer program for ex-convicts. Reporting this to the sheriff, David confronts Vick, who is arrested at the funeral. Vick agrees to confess, in exchange for leniency for her son, Robert. Having a crush on Margot, Robert used the YouCast account under the name Hannah to get close to her. Margot sent money to Robert's Venmo account, believing he was a working-class girl whose mother had cancer. Ashamed for lying, Robert wanted to return the money in person and followed her to Barbosa Lake to reveal himself. He surprised her by getting into her car, and she ran, with him accidentally pushing her off a cliff into a 50-foot-deep ravine. Assuming the accident was fatal and could be perceived as manslaughter or even first-degree murder, Vick decided to cover up the incident, pushing the car into the lake and fabricating the fake ID evidence to make it look like Margot ran away. After David found the car, Vick turned Cartoff into the fall guy and staged his confession. Vick says that Margot is still in the ravine, suggesting that even if she had survived the fall, she could not have lived five days without water. David tells the police to return to the ravine, remembering the storm on the third day of the search, which could have provided her with water. The rescue crew finds Margot severely injured but alive. Two years later, Margot applies for college to major in piano. David tells her Pamela would have been proud of her. Margot changes her desktop picture from one of Pamela and her to the one David sent her of the two of them in the school hallway after the rescue, reflecting a closer relationship between them.

Four real-estate salesmen (Richard Roma, George Aaronow, Shelley "The Machine" Levene, and Dave Moss) are supplied with leads—the names and phone numbers of prospective investors—and use deceitful and dubious sales tactics. Many of the leads rationed by office manager John Williamson lack either the money or the desire to actually invest in land. The firm sends Blake, one of its top salesmen, to motivate the team. In a torrent of verbal abuse, he gives them notice of termination and tells them that only the top two deal-closers of the month, with one week to go, will keep their jobs and gain access to promising leads for the new and lucrative Glengarry Highlands development. Levene is a once-successful salesman in a long-running slump and with a daughter in the hospital. Levene tries to persuade Williamson to give him some of the Glengarry leads. Williamson is willing to sell some of the prime leads, but demands cash in advance, which Levene does not have. Moss and Aaronow complain about the firm's management, and Moss proposes that they steal the Glengarry leads and sell them to a competing agency. Aaronow wants no part of the plan, but Moss tries to coerce him, saying that Aaronow is already an accessory before the fact because he knows about the proposed burglary. Roma, the office's top closer, manipulates a meek, middle-aged man named James Lingk into buying property. Framing the deal as an opportunity rather than a purchase, Roma plays on Lingk's feelings of insecurity. The next day, when the salesmen arrive at the office, they learn that there has been a burglary and that the Glengarry leads have been stolen. Williamson assures Roma that his contract with Lingk was not stolen, and he and the police question each of the salesmen in private. After his interrogation, Moss has a shouting match with Roma and leaves. Lingk arrives to demand the return of his down payment under the three-day cooling-off period because his wife objects to the deal. Roma tries to stall and confuse Lingk but is interrupted by the police detective, who wants to question him. He lies to Lingk, telling him that the check has not yet been cashed and that there is time to cancel the payment when he returns from a trip on Monday. Williamson, who is unaware of the tactic, contradicts him, causing Lingk to rush out of the office upset. Roma berates Williamson for ruining his sale, unaware that Williamson also lied to him and the check was not cashed. Levene, proud of a big sale that he made that morning, also berates Williamson for "making something up" without knowing the situation. Williamson realizes that Levene could only have known he lied about the check being cashed if he broke into the office and saw the check on his desk (as he, in practice, always takes the checks immediately to the bank at the end of the night), and threatens to inform the police if he does not return the leads. Levene admits that he sold the leads to a competitor and split the money with Moss. Levene attempts to bribe Williamson with a share of his sales to keep quiet, but Williamson scoffs that Levene has no sales. He already knows Levene's latest buyers are a delusional couple who have no money. Levene realizes he has been set up to fail by being given a worthless lead, and asks Williamson why, to which Williamson replies "because I don't like you." Levene pleads for his ill daughter, but Williamson rebuffs him and leaves to inform the detective. Roma emerges from questioning. Unaware of the exchange, he compliments Levene on his sale and suggests that they form their own partnership. As Levene gets up to meet with the detective, he looks back wistfully at Roma, who has already returned to his sales work. Aaronow picks up the phone and calls a lead.

In 1958, 15-year-old Michael Berg becomes sick on a tram ride in an unnamed provincial city. He is helped by 36-year-old tram conductor Hanna Schmitz. Weeks later, Michael has recovered from scarlet fever and at his mother's insistence, he visits Hanna with flowers to thank her for her help. They proceed to have a secret summer love affair, and Hanna often asks Michael to read to her. They have a brief cycling holiday in the country where Michael starts to notice some oddities in Hanna's behaviour. However, as their sexual relationship deepens it grows more tumultuous, when his attempts to form a deeper connection are rebuffed by her secretive nature. As a good reliable worker, Hanna is soon promoted, whereupon she abruptly quits without explanation. Michael visits Hanna to apologize following an argument, but is utterly befuddled and devastated to find her apartment vacant. In 1966, Michael is a student at Heidelberg University Law School and observes a war crime trial of several former female SS guards accused of letting 300 Jewish women and children perish in a burning church during a death march near Kraków in Poland. Michael is horrified to learn Hanna is one of the defendants. Survivor Ilana Mather provides testimony, including that Hanna forced some of the prisoners to read to her. Hanna admits that she and the co-defendants each chose ten women monthly for extermination at Auschwitz in Nazi-occupied Poland. Ilana's mother Rose testifies that when the church caught fire during a bombing, the guards refused to unlock the doors. The official SS report stated the guards did not know about the fire until the following day. Hanna reveals the guards in fact kept the doors locked so that the prisoners could not escape. Hanna's co-defendants all state she was in command and wrote the report. Hanna denies this, insisting they agreed on the contents of the report together. When the lead judge asks for a handwriting sample, Hanna quickly condemns herself by admitting she authored the report alone. Recalling their time together, Michael is initially confounded by her testimony, finally deducing that Hanna is deeply ashamed of being illiterate. Michael informs his law professor, who states that Michael should inform the court. Deeply conflicted, Michael attempts to visit Hanna in prison, but changes his mind. Hanna receives a sentence of life imprisonment, while her co-defendants are sentenced to just over four years each. Michael attempts to move on, though haunted by the memories of a relationship that he cannot put to rest. He marries and has a daughter, however, Michael cannot commit fully to the relationship and grows distant from his family, culminating in divorce and estrangement from his daughter, Julia. Throughout the 1980s, Michael records himself on tape reading various books and regularly mails them to Hanna. Borrowing the same books from the prison library, Hanna slowly teaches herself to read and write. She starts writing to Michael, but he never replies. In 1988, a prison official requests Michael's help with Hanna's parole as he has been the only person outside prison to have had contact with her. Michael finally visits Hanna, revealing in the stilted reunion that he has secured her a residence and a job. When Michael arrives for Hanna's release, he is told she hanged herself in her cell and left a crude will asking Michael to give her money to Ilana Mather. Michael finds Ilana in New York City, revealing his connection to Hanna and its long-lasting impact. He tells Ilana about Hanna's illiteracy, but she rebuffs this and refuses to forgive Hanna. Michael gives her Hanna's tea tin filled with cash, but Ilana refuses the money. He suggests it be donated to a Jewish literacy organization in Hanna's name and Ilana agrees. She keeps the tin, placing it next to a photograph of her deceased family. The film ends in 1995 with Michael driving Julia to Hanna's grave, telling her their story.

David Gale is a former professor on death row in Texas. With only a few days until his execution, his lawyer negotiates a half-million-dollar fee to tell his story to Bitsey Bloom, a journalist from a major news network. She has a reputation for keeping secrets and protecting her sources. He tells her his story, revealed through a series of flashbacks. In 1994, Gale is a successful intellectual and the head of the philosophy department at the fictional University of Austin (not to be confused with the present day and then non-existent University of Austin). He is an active member of DeathWatch, an advocacy group campaigning against capital punishment. At a graduation party, he encounters Berlin, a graduate student who has been expelled from the school. When Gale gets drunk, she seduces him, and they have rough sex. She then falsely accuses Gale of rape. The next day, he loses a televised debate with the Governor of Texas when he is unable to name any innocent people executed during the governor's term. Gale is arrested, but the charge is dropped when Berlin disappears. However, his marriage, career, and reputation are all destroyed. Gale struggles with alcoholism after his wife Sharon takes their son with her to Spain and disallows contact. Constance Harraway, a fellow DeathWatch activist, is a close friend of Gale who consoles him after his life falls apart. However, Harraway is discovered raped and murdered, suffocated by a plastic bag taped over her head. An autopsy reveals Gale's semen in her body and that she had been forced to swallow the key to the handcuffs, a Securitate torture technique which Gale previously wrote about. The physical evidence at the crime scene points to Gale, who is convicted of rape and murder and is sentenced to death. In the present, Bloom investigates the case between her visits with Gale. Gale maintains his innocence, claiming he and Harraway had consensual sex the night before her murder. Bloom comes to believe that the apparent evidence against Gale does not add up. She is tailed several times in her car by Dusty Wright, an alleged one-time lover and colleague of Harraway, whom she suspects was the real killer. Wright slips evidence to Bloom that suggests Gale has been framed, implying that the actual murderer videotaped the crime. Bloom pursues this lead until she finds a tape revealing that Harraway, who was suffering from terminal leukemia, had committed an elaborate suicide made to look like murder. Wright is seen on the videotape, acting as her accomplice, implying that they framed Gale as part of a plan to discredit the death penalty by conspiring to execute an innocent person, and subsequently releasing evidence of the actual circumstances. Once Bloom and her aide find this evidence, only hours remain until Gale's scheduled execution. She tries to give the tape to the authorities in time to stop the execution. She arrives at the Huntsville Unit just as the warden announces that the execution has been carried out. The tape is subsequently released, causing an uproar over the execution of an innocent man. Later, Wright receives the money that Bloom's magazine agreed to pay for the interview and delivers it to Sharon, along with a postcard from Berlin confessing that the rape accusation that derailed Gale's life and career was false. Sharon looks distraught, knowing Gale told the truth and that she effectively stole their child away from him. Later, a videotape labeled "Off the Record" is delivered to Bloom. This tape shows Harraway's suicide and Gale deliberately leaving his fingerprints on the plastic bag in the process. He then looks at the camera and ends the recording, leaving Bloom stunned with the truth that the couple deliberately sacrificed themselves to discredit capital punishment.

In 2200, Aline Ruby, a private detective, and Carlos Rivera, an android replica of her partner who died five years earlier, are sent to Earth to capture Roberta Williams, a robot-hacking criminal. Back on Mars, Roberta's arrest warrant has disappeared and she is released. A new investigation is entrusted to the duo: to track down Jun Chow, a cybernetics student known for illegally jailbreaking androids who, like her roommate, has gone missing. Aline and Carlos venture to the depths of Noctis, the main terrestrial establishment of Mars created thanks to the progress of robotics, and where humans and various forms of androids seem to coexist in harmony. The city turns out to hide secrets such as trafficking and clandestine computer labs. Meanwhile, activists try to free the robots from the security constraints that bind them to humans. Ultimately, the robots are successfully emancipated and revolt, but peacefully, by uploading their consciousnesses to computers aboard spaceships and thus escaping to space. Carlos, grief-stricken by the loss of his partner and realizing that he is a dead consciousness embodied in a machine who has been "trying to hold onto a life that's moved on without him", decides to go with the robots.

On 29 April, Sergeant Neil Howie of the West Highlands Constabulary journeys by seaplane to the remote, verdant Hebridean island of Summerisle to investigate the disappearance of a young girl, Rowan Morrison, about whom he has received an anonymous letter. Howie, a devout Christian, is disturbed to find the islanders paying homage to the pagan Celtic gods of their ancestors, with churches having fallen into disuse. They copulate openly in the fields, include children as part of the May Day celebrations, teach children of the phallic association of the maypole, and one places a toad in a child's mouth to cure a sore throat. The islanders appear to be trying to thwart his investigation by claiming that Rowan never existed. While Howie is staying at the Green Man Inn, the landlord's daughter attempts to seduce him, but he resists, explaining that he is engaged and must reserve sex for marriage. He notices a series of photographs celebrating the annual harvest, each featuring a young girl as the May Queen. The photograph of the most recent celebration is missing and the landlord tells him it was broken. At the local school, Howie asks the students about Rowan, but all deny her existence. He checks the school register and finds Rowan's name. He questions the schoolteacher, who directs him to Rowan's grave. The next day, 30 April, Howie meets the island's leader, Lord Summerisle, grandson of a Victorian agronomist, to get permission to exhume Rowan's body. Summerisle explains that in 1868, his grandfather developed strains of fruit trees that would prosper in Scotland's climate and encouraged the belief that returning to the old gods would bring prosperity to the island among the previously Christian population. Due to the bountiful harvests, the island's other inhabitants gradually embraced paganism, and the Christian ministers fled to the mainland. Exhuming Rowan's grave, Howie finds that the coffin contains only the body of a hare. He also finds the missing harvest photograph, showing Rowan standing amidst empty boxes; the harvest had failed for the first time since the orchards were established. His research reveals that a human sacrifice is offered to the gods in the event of crop failure. He concludes that Rowan is alive and will soon be sacrificed to ensure a successful harvest this season. The following morning, on May Day, Howie seeks assistance from the mainland and returns to his seaplane, only to discover it no longer functions and its radio is damaged; he cannot leave or call for help. Later that day, during the May Day celebration, Howie subdues the innkeeper and steals his costume and mask of Punch (the Fool) to infiltrate the parade, involving a long sword dance. Rowan is eventually revealed. Howie sets her free and flees with her into a cave. Exiting it, they are intercepted by the islanders, to whom Rowan happily returns. Summerisle tells Howie that Rowan was never the intended sacrifice — Howie is. He fits their gods' four requirements: he came of his own free will, he has "the power of a king" by representing the law, he is a virgin, and he is a "fool" by falling for their deception. Howie warns Summerisle and the islanders that the crops are failing due to the unsuitability of the climate, and that the villagers will turn on Summerisle and sacrifice him next summer when the harvest fails again, but his pleas are ignored. The villagers force Howie inside a giant wicker man statue along with various animals, set it ablaze, and surround it, singing the Middle English folk song " Sumer Is Icumen In ". Inside the wicker man, Howie recites Psalm 23 and prays to God. Howie and the animals burn to death as the head of the wicker man collapses in flames, revealing the setting sun.

In January 1994, the U.S. Ohio -class submarine USS Montana has an encounter with an unidentified submerged object, and sinks near the Cayman Trough. With Soviet ships moving in to try to salvage the sub, and a hurricane moving over the area, the U.S. government sends a SEAL team to Deep Core, a privately owned, experimental underwater drilling platform near the Cayman Trough, to use it as a base of operations. The platform's designer, Dr. Lindsey Brigman, insists on going along with the SEAL team, even though her estranged husband, Virgil "Bud" Brigman, is the current foreman. During the initial investigation of Montana, a power cut in the team's submersibles leads to Lindsey seeing a strange light circling the sub, which she later calls a "non-terrestrial intelligence", or "NTI". Lt. Hiram Coffey, the SEAL team leader, is ordered to accelerate their mission, and takes one of the mini-subs, without Deep Core ' s permission, to recover a Trident missile warhead from Montana, just as the storm hits above, leaving the crew unable to disconnect from their surface support ship in time. The cable crane is torn from the ship and falls into the trench, dragging Deep Core to the edge before it stops. The rig is partially flooded, killing several crew members, and damaging its power systems. The crew waits out the storm so they can restore communications and be rescued. As they struggle against the cold, they find the NTIs have formed an animated column of water to explore the rig, which they equate to an alien version of a remotely operated vehicle. Though they treat it with curiosity, Coffey is agitated and cuts it in half by closing a pressure bulkhead on it, causing it to retreat. Realizing that Coffey is experiencing paranoia as a result of suffering from high-pressure nervous syndrome, the crew spies on him through an ROV, finding him, along with another SEAL, arming the warhead to attack the NTIs. To try to stop him, Bud fights Coffey, but Coffey escapes in a mini-sub with the primed warhead. Bud and Lindsey give chase in the other sub, damaging both. Coffey is able to launch the warhead into the trench, but his sub drifts over the edge and implodes from the pressure, killing him. Bud's mini-sub is inoperable and taking on water. With only one functional diving suit, Lindsey opts to drown and hopefully enter deep hypothermia when the ocean's cold water engulfs her, with hopes of being able to be resuscitated. Bud swims back to the platform with her body; there, he and the crew use a defibrillator and administer CPR, and they revive her. It is decided that they need to disarm the warhead, which is more than 2 miles (3.2 km) below them. One SEAL, Ensign Monk, helps Bud use an experimental diving suit equipped with a liquid breathing apparatus to survive to that depth, though he will only be able to communicate through a keypad on the suit. Bud begins his dive, assisted by Lindsey's voice to keep him coherent against the effects of the mounting pressure, and he reaches the warhead. Monk guides him in successfully disarming it. With little oxygen left in the system, Bud explains that he knew it was a one-way trip, and he tells Lindsey he loves her. As he waits for death, an NTI approaches Bud, takes his hand, and guides him to a massive alien city deep in the trench. Inside, the NTIs create an atmospheric pocket for Bud, allowing him to breathe normally. The NTIs then play back Bud's message to his wife and look at each other with understanding. On Deep Core, the crew is waiting for rescue when they see a message from Bud that he met some friends and warns them to hold on. The base shakes, and lights from the trench herald the arrival of the alien ship. It rises to the ocean's surface, with Deep Core and several of the surface ships run aground on its hull. The crew of Deep Core exits the platform, surprised they are not dead from the sudden decompression. They see Bud walking out of the alien ship, and Lindsey races to hug him.

U.S. Army pilot Captain Colter Stevens wakes up on a Metra commuter train going into Chicago. He is disoriented, as his last memory was of flying a mission in Afghanistan. However, to the world around him – including his friend Christina Warren and his reflection in the train's windows and mirrors – he appears to be a different man: a school teacher named Sean Fentress. As he expresses his confusion to Christina, the train explodes while passing another train, killing everyone aboard. Stevens abruptly awakens in a dimly lit cockpit. Communicating through a video screen, Air Force Captain Colleen Goodwin verifies Stevens' identity and tells him of his mission to find the train bomber before sending him back to the moment he awoke on the train. Believing he is being tested in a simulation, Stevens finds the bomb in a vent inside the lavatory but is unable to identify the bomber. Still thinking he is in a simulation, Stevens leaves the bomb and goes back down to the main cabin before the train explodes again. Stevens again reawakens in his capsule and after demanding to be briefed, learns that the train explosion actually happened and that it was merely the first attack of a suspected series. He is sent back yet again, eight minutes before the explosion, to identify the bomber. This time, he disembarks from the train (with Christina) to follow a suspect. This turns out to be a dead end, the train still explodes in the distance, and Stevens is killed by a passing train after falling onto the tracks while interrogating the suspect. The capsule power supply malfunctions as Stevens reawakens. He claims to have saved Christina, but Dr. Rutledge, head of the project, tells him that she was saved only inside the "Source Code". Rutledge explains that the Source Code is an experimental machine that reconstructs the past using the dead passengers' residual collective memories of eight minutes before their deaths. Therefore, the only thing that matters is finding the bomber to prevent the upcoming second attack in Chicago. On the next run, Stevens learns that he was reported as killed in action two months earlier. He confronts Goodwin, who reveals that he is missing most of his body, is on life support, and is hooked up to neural sensors. The capsule and his healthy body are "manifestations" made by his mind to make sense of the environment. Stevens is angry at this forced imprisonment. Rutledge offers to terminate him after the mission, and Stevens eventually accepts. After numerous attempts, including being arrested by train security for trying to obtain a weapon, Stevens identifies the bomber through a fallen wallet as the nihilistic domestic terrorist Derek Frost. He memorizes Frost's license and vehicle registration plates, and discovers a dirty bomb built inside a van owned by Frost; Christina follows him, and Frost shoots both of them dead. Outside the Source Code, Stevens relays his knowledge to Goodwin, which helps the police arrest Frost and prevents the second attack. He is congratulated for completing his mission. Rutledge secretly reneges on his deal to let Stevens die, as he is still the only candidate able to enter the Source Code. Being more sympathetic to his plight, Goodwin sends Stevens back one last time and promises to disconnect his life support after eight minutes. This time, he sets a date with Christina, defuses the bomb, apprehends Frost, and reports him to the police. He calls his father under the guise of a fellow soldier and reconciles with him, and sends Goodwin an email. After eight minutes, Goodwin terminates Stevens's life support. As the world around him continues to progress beyond eight minutes, Stevens confirms his suspicion that the Source Code is not merely a simulation, but rather a machine that allows the creation of alternate timelines. He and Christina leave the train and go on a date. In the same (alternate) reality, Goodwin receives Stevens's message. He tells her of the Source Code's true capability and asks her to help the alternate-reality version of him.

Astronomer Dr. Ellie Arroway arrives at the SETI program at the Arecibo Observatory in Puerto Rico. The film's prologue reveals that she was encouraged to pursue science by her father, who died in her youth. In the film's present, Arroway studies radio emissions from space to detect signs of intelligent extraterrestrial life. While in Puerto Rico, Arroway meets Christian philosopher, Palmer Joss. They have a brief romantic encounter, but Arroway does not contact him again. David Drumlin, the President's science advisor, cuts SETI funding, deeming it futile. Arroway is furious and instead pursues and receives financial support from S. R. Hadden, a reclusive billionaire industrialist. Arroway re-locates her team to the Very Large Array (VLA) radio dish observatory in New Mexico. Four years later, Arroway is about to lose access to the VLA satellite dishes. Before being evicted, she discovers a signal containing a sequence of prime numbers originating from the star Vega. Drumlin and the National Security Council, headed by Michael Kitz, arrive and attempt to federalize the facility. Meanwhile, Arroway's team detect a video embedded within the signal: Adolf Hitler 's opening address at the 1936 Summer Olympics in Berlin, Germany. The Hitler transmission was the first to penetrate the Earth's ionosphere and reach Vega. The project is put under federal security and its progress is monitored globally. It is discovered that the signal contains over 63,000 pages of encoded data, though it is undecipherable without a primer. Hadden breaches the government's computer systems and discovers the primer, providing Arroway the means to decode the data. It reveals schematics for what could be a transportation device for a single person. Multiple nations provide funding for the construction at the Kennedy Space Center in Cape Canaveral. An international panel is assembled to select a candidate to travel in the machine. An American is preferred, and Arroway is a leading candidate until Palmer Joss, a panel member, focuses on her atheism during the interviews. The panel selects Drumlin. During the first tests, a fanatical religious terrorist destroys the machine with a suicide bomb, killing Drumlin and several others. Hadden, terminally ill with cancer, is now residing on the Mir space station. He informs Arroway that the US government and Hadden Industries have secretly built a second machine in Hokkaido, Japan. Arroway, the only remaining American candidate, will use it. In Japan, Joss and Arroway are reunited. Joss explains he voted against Arroway because he feared she would not survive the experiment. Equipped with multiple recording devices, Arroway enters a pod which is dropped through the massive machine's counter-rotating rings. She seemingly travels through wormholes and observes a radio array-like structure at Vega, signs of civilization on an alien planet, and a celestial event. Arroway finds herself on a beach similar to her childhood drawing of Pensacola, Florida. An alien assuming her deceased father's appearance approaches. He explains that the aliens detected humans' radio emissions and judged it worthy of a first step into the cosmos. Arroway is soon sent back through the wormhole. Arroway regains consciousness inside the pod. The mission control team reports that the pod fell through the machine into a safety net and that the experiment achieved nothing. Arroway insists she was gone for hours, but her devices recorded only static. A Congressional Committee headed by Kitz speculates the signal and the machine were a hoax perpetrated by Hadden, now deceased. Arroway admits she cannot scientifically prove her experience and requests the committee accept her testimony on faith. Joss tells the press that he believes Arroway's claim, and they leave the hearing together. Kitz and White House official Rachel Constantine discuss the confidential information and observe that Arroway's device recorded 18 hours of static. Arroway receives ongoing financial support for the SETI program at the VLA.

Dr. Bill Harford and his wife Alice live in New York City with their daughter, Helena. At a Christmas party hosted by Bill's patient, Victor Ziegler, Bill reconnects with his former medical school classmate, Nick Nightingale, now a professional pianist. Meanwhile, an older Hungarian guest attempts to seduce Alice, while two young models try to seduce Bill. Victor interrupts Bill's flirtation to handle an emergency involving Mandy, a young woman who overdosed during sex with him. Bill helps stabilize Mandy. The following night, Bill and Alice smoke marijuana and discuss their unfulfilled desires. Bill dismisses the idea of Alice being unfaithful, believing women to be naturally loyal. However, Alice shocks him by confessing to fantasizing about a naval officer she observed while on vacation, even considering leaving Bill and Helena for him. Disturbed, Bill is called to a patient's home, where the patient's daughter, Marion, confesses her love and tries to seduce him. Bill resists and leaves. Wandering the city, Bill meets a prostitute named Domino. Before anything happens, Alice calls, prompting Bill to leave after paying Domino without proceeding further. Later, Bill encounters Nick at a jazz club. Nick tells Bill about a secretive late-night gig where he will play piano blindfolded, and reveals the password to gain entry. Intrigued, Bill visits a costume store, formerly owned by one of his patients but now run by Mr. Milich, to rent an outfit. During the visit, Milich discovers his teenage daughter with two older men and locks the men in a room, threatening to call the police. Bill arrives at the mansion, provides the password, and witnesses a bizarre sexual ritual. A masked woman warns him that he is in danger. He is taken to a gathering where the master of ceremonies demands a second password. Bill claims to have forgotten the second password, at which the master of ceremonies exposes him as an outsider. Before the master of ceremonies forces Bill to remove his clothes, the masked woman intervenes, offering herself to save him. Bill is let go with a stern warning to remain silent. Shaken, Bill returns home to find Alice laughing in her sleep. She tearfully recounts a dream of having sex with the naval officer and many other men while mocking Bill. The next day, Bill visits Nick's hotel, but the clerk claims Nick was taken away by two threatening men. Returning the costume, Bill notices the mask is missing and learns that Milich now profits from prostituting his daughter, offering her services to Bill. Consumed by jealousy and doubt, Bill revisits the mansion but receives an envelope warning him to stay away. That evening, he tries calling Marion but hangs up when her fiancé answers. He then visits Domino's apartment, only to find her roommate, Sally, who informs him that Domino has tested HIV-positive. As Bill leaves, a mysterious figure follows him. Later, at the morgue, he identifies Mandy as the masked woman from the orgy after reading about her death from an overdose. Victor summons Bill and admits to being at the orgy. He explains that there was no second password and that Bill's exposure was deliberate. Victor insists the secret society only seeks to intimidate him into silence but warns they are dangerous. He claims Nick has returned safely to Seattle and attributes Mandy's death to her drug addiction, dismissing foul play. Returning home, Bill finds the missing mask placed on his pillow. Breaking down in tears, he confesses everything to Alice. The next day, the couple takes Helena shopping for Christmas. Bill apologizes to Alice, who suggests they take action to repair their relationship. When he asks what she means, Alice responds with a single word: "Fuck."