The story is set in the early 1970s, ten years in the future at the time of the film's 1964 release, and the Cold War is still a problem (in the 1962 book, the setting was May 1974). U.S. President Jordan Lyman has recently signed a nuclear disarmament treaty with the Soviet Union, and the subsequent ratification has produced a wave of public dissatisfaction, especially among the President's opposition and the military, who believe the Soviets cannot be trusted.
In September 1942, U.S. Army Corps of Engineers General Leslie Groves (Paul Newman) who oversaw construction of the Pentagon is assigned to head the ultra-secret Manhattan Project, to beat the Germans in building an atomic bomb.
When the Japanese freighter Eiko-maru is destroyed near Odo Island, the Bingo-maru is sent to investigate, only to meet the same fate with few survivors. A fishing boat from Odo is also destroyed, with one survivor. Fishing catches mysteriously drop to zero, blamed by an elder on the ancient sea creature known as "Godzilla". Reporters arrive on Odo Island to further investigate. A villager tells one of the reporters that "something large is going crazy down there" ruining the fishing. That evening, a ritual dance to appease Godzilla is held during which the reporter learns that the locals used to sacrifice young girls. That night, a large storm strikes the island, destroying the reporters' helicopter, and an unseen force destroys 17 homes, kills nine persons and 20 of the villagers' livestock.
An expedition to an irradiated island brings civilization in contact with a primitive native culture. When one sensationalist entrepreneur tries to exploit the islanders, their ancient deity arises in retaliation.
New Mexico State Police troopers Ben Peterson (James Whitmore) and Ed Blackburn (Chris Drake) discover a little girl in shock, wandering the desert near Alamogordo, New Mexico. They retrace her steps to a mobile home owned by an FBI agent named Ellinson, who was on vacation in the area with his family. The side of the trailer was ripped open from the outside, the rest of the family is missing and no money was taken. A single unidentifiable animal track seems to be the only clue. Then a strange, pulsating high-pitched noise echos out of the desert on the wind. The little girl briefly reacts in fear when she hears the sound, but this is not noticed by those around her.
In early 1950s southern California, Dr. Clayton Forrester (Gene Barry), a scientist who had worked on the Manhattan Project, is fishing with colleagues when a large object crashes near the town of Linda Rosa. At the impact site, he meets Sylvia Van Buren (Ann Robinson) and her uncle, Pastor Matthew Collins (Lewis Martin). Van Buren was told that the meteorite came down at a low angle, while Forrester observes it appears far lighter than normal for its massive size. His Geiger counter also detects it is slightly radioactive, but the object is still too hot to examine closely. Unable to account for these anomalies, Forrester is intrigued and decides to wait in town overnight for the object to cool down.
In 1945, physicist and atomic scientist Dr. J. Robert Oppenheimer (Hume Cronyn) praises the discovery of atomic energy, but also warns of its dangers. American scientists such as Matt Cochran (Tom Drake), working under the guidance of Dr. Enrico Fermi (Joseph Calleia) and Dr. Marré (Victor Francen), have split the atom, and essentially beaten the Germans in the race to create an atomic bomb. With the assistance of Albert Einstein (Ludwig Stössel), they inform President Franklin D. Roosevelt (Godfrey Tearle) that a monumental discovery has been made.
In the small mining village of Kitamatsu, on the southern Japanese island of Kyushu, two miners have gone missing. The two men, Goro and Yoshi, had brawled earlier that day, and after they entered the mine to start their shift, the shaft had quickly flooded. Shigeru Kawamura (Kenji Sahara), a tunneling and safety engineer at the mine, heads below to investigate and makes a gruesome discovery: Yoshi's lacerated corpse. Above ground, a doctor examines Yoshi, and discovers the cause of death to be a series of deep gashes caused by an abnormally sharp object. Some of the miners and their families begin to discuss the possibility of the involvement of Goro, who is still unaccounted for, in the death. Shigeru is personally affected by this incident, since his fiancée Kiyo (Yumi Shirakawa) is also Goro's sister.
The film takes place in a single day and night. The film opens with the two main characters, Harry (Anthony Edwards) and Julie (Mare Winningham), meeting at the La Brea Tar Pits and immediately falling in love. After spending the afternoon together, they make a date to meet after her shift ends at midnight at a local coffee shop, but a power failure means Harry's alarm fails to wake him and Julie leaves for home.
African-American coal mine inspector Ralph Burton (Harry Belafonte) becomes trapped underground in a cave-in while inspecting a mine in Pennsylvania. He can hear rescuers digging towards him, but after a few days they slow down and then stop completely. Alarmed, he digs his own way out. Reaching the surface, he finds a deserted world. (No bodies are seen at any time in the film.) Some discarded newspapers provide an explanation: one proclaims "UN Retaliates For Use Of Atomic Poison", another that "Millions Flee From Cities! End Of The World". Ralph later plays tapes at a radio station that an unknown nation had used radioactive isotopes as a weapon, yielding a dust cloud that spread globally and was completely lethal for a five-day period.
An atomic war has seemingly destroyed most (if not all) human civilization, leaving Earth contaminated with radioactive fallout. The apparent single exception is a box canyon, surrounded by lead-bearing cliffs, in which former Navy Commander Jim Maddison lives with daughter Louise (Lori Nelson) in a home stocked with supplies anticipating just such a holocaust. Louise is engaged to be married, but her fiance is missing.
The film opens on the birthday of Alexander (Erland Josephson), an actor who gave up the stage to work as a journalist, critic, and lecturer on aesthetics. He lives in a beautiful house with his actress wife Adelaide (Susan Fleetwood), stepdaughter Marta (Filippa Franzén), and young son, "Little Man", who is temporarily mute due to a throat operation. Alexander and Little Man plant a tree by the sea-side, when Alexander's friend Otto, a part-time postman, delivers a birthday card to him. When Otto asks, Alexander mentions that his relationship with God is "nonexistent". After Otto leaves, Adelaide and Victor, a medical doctor and a close family friend who performed Little Man's operation, arrive at the scene and offer to take Alexander and Little Man home in Victor's car. However, Alexander prefers to stay behind and talk to his son. In his monologue, Alexander first recounts how he and Adelaide found this lovely house near the sea by accident, and how they fell in love with the house and surroundings, but then enters a bitter tirade against the state of modern man. As Tarkovsky wrote, Alexander is weary of "the pressures of change, the discord in his family, and his instinctive sense of the threat posed by the relentless march of technology"; in fact, he has "grown to hate the emptiness of human speech".
Set in 2008, President Walter Emerson, formerly an appointed Vice President and elevated by the death of the previous (unseen) commander-in-chief, is crossing the country on a campaign tour when a freak snowstorm traps him in a remote Colorado diner with members of his staff plus a group of ordinary citizens.
In 1957, the Soviet Union attacks the United States with nuclear weapons, rendering most of the nation uninhabitable. The American government has collapsed with the exception of the haven known as "Lost Vegas", ruled by King Elvis. The Red Army has been besieging Lost Vegas, but the lack of supplies over the years has relegated them to a gang of thugs. Forty years after the Soviet invasion, King Elvis dies and radio disc jockey Keith Mortimer announces a call for all musicians to come to Lost Vegas to try to become the new King of Rock 'n' Roll.
James and Hilda Bloggs are a retired couple living in a tidy isolated cottage in rural Sussex in southeast England. James frequently travels to London to read the newspapers and keep abreast of the deteriorating international situation; while frequently misunderstanding some specifics, he is fully aware of the growing risk of a nuclear war with the Soviet Union. James is horrified at a radio news report stating that a war may be only three days away, and sets about preparing for the worst as instructed by his government-issued Protect and Survive pamphlets. As Hilda continues her daily routine, and their son Ron dismisses such preparations as pointless (referencing the song "We'll All Go Together When We Go" by Tom Lehrer), James builds a lean-to shelter inside their home (which he consistently calls the "inner core or refuge" per the pamphets) and prepares a stock of supplies. He also follows through seemingly strange instructions such as painting his windows with white paint and readying sacks to lie down in when a nuclear strike hits. Despite James' concerns, he and Hilda are confident they can survive the war, as they did World War II in their childhoods, and that a Soviet defeat will ensue.