In Aroostook County, Maine, marine Fish and Game officer Walt Lawson is attacked and bitten in half by something unseen in Black Lake. Sheriff Hank Keough (Brendan Gleeson), Fish and Game officer Jack Wells (Bill Pullman), American Museum of Natural History paleontologist Kelly Scott (Bridget Fonda), and mythology professor/crocodile enthusiast Hector Cyr (Oliver Platt) go to the lake to investigate.
The film begins with Emil Slovak (Karel Roden) and Oleg Razgul (Oleg Taktarov) arriving in America. They were former criminals and after getting out of prison have come to the U.S. to claim their part of a bank heist in Russia (or somewhere in Czech Republic). Within minutes of arriving, Oleg steals a video camera. They go to the run down apartment of their old partner and demand their share. He doesn't have it so Emil stabs him and his wife to death, as Oleg tapes it with the camera. The couple's friend, Czech immigrant Daphne Handlova (Vera Farmiga), covertly witnesses the murders from the bathroom, but she escapes before they can get her too. To hide the crime, Emil burns down the apartment.
In 1991 in New York City, 11-year-old Alyssa "Ally" Craig is waiting with her mother for the subway on the F Line at 18th Avenue and McDonald Avenue. Suddenly, the pair are mugged by two young men who then shoot her mother before boarding the train. Ally is left scarred by the events and refuses to travel by subway again.
Nine-year-old Oskar Schell (Thomas Horn) is the son of German American Thomas Schell (Tom Hanks). Thomas would often send Oskar on missions to do something involving one of his riddles. The last riddle he ever gives Oskar is proof that New York City once possessed a Sixth Borough. In a flashback, Thomas and Oskar play a scavenger hunt to find objects throughout New York City. The game requires communication with other people and is not easy for the socially awkward Oskar who is told "If things were easy to find, they wouldn't be worth finding".
The United States is devastated by a mysterious phenomenon which reanimates recently deceased unburied human beings as flesh-eating zombies. Despite the best efforts by the U.S. government and local authorities to control the situation, society is beginning to collapse and the remaining survivors are given to chaos. Some rural communities and the military have been effective in fighting the zombies in open country, but cities are helpless and largely overrun. Confusion reigns at the WGON television studio in Philadelphia by the phenomenon's third week, where staff members Stephen Andrews and Francine Parker are planning to steal the station's traffic helicopter to escape the zombies. Meanwhile, police SWAT officer Roger DiMarco and his team raid an apartment building where the residents are defying the martial law of delivering their dead to National Guardsmen. Some residents fight back with handguns and rifles, and are killed by both the overzealous SWAT team and their own reanimated dead. During the raid, Roger meets Peter Washington, part of another SWAT team, and they partner up together. Roger tells Peter that his friend Stephen intends to take his network's helicopter, and suggests that Peter come with them. The matter is decided when they are informed of a group of zombies sheltered in the basement, which they execute with grim determination.
In the town of Ogden Marsh, Iowa, David Dutten (Timothy Olyphant), the local sheriff is enjoying a baseball game. His deputy, Russell Clank (Joe Anderson), spots Rory Hamill, a local resident (and the town drunk who's has been sober for two years), entering the outfield holding a shotgun. David, knowing his history, and owing to his behaviour, believes he has started drinking again. David is forced to shoot and kill the unresponsive Rory when he raised his weapon and aimed it at the Sheriff. David and his wife Judy (Radha Mitchell), the community doctor, begin to notice other town residents exhibiting bizarre behavior, including listlessness and repetitive speech. The next night, a local farmer burns his house down with his wife and son trapped inside, killing them. By the time firefighters and other townspeople arrive, he is found mowing his lawn while his house burns.
Daniel Kintner (Daniel Travis) and Susan Watkins (Blanchard Ryan) are a couple frustrated that their hard-working lives do not allow them to spend much time together. They decide to head out on a scuba-diving vacation to help improve their relationship. On their second day, they join a group scuba dive. A head count is taken, and the passenger total is recorded as 20. Daniel and Susan decide to separate briefly from the group while underwater. Half an hour later, the group returns to the boat. Going by the tally sheet, the total comes to 20, though in reality, it is 18. Daniel and Susan are still underwater and have not yet realized that the others have returned. The boat leaves the site. Not long after, Daniel and Susan return to the surface and look for it. They believe the group will return to recover them in reasonable time.
The rescue mission took place in 1952 off the Cape Cod coast after two oil tankers, SS Fort Mercer and SS Pendleton, were destroyed by treacherous winter winds and waves. The crew of motor life boat CG 36500 and the crew of a surfboat from the USCGC Yakutat heroically rescued nearly all the tankers' crewmen.
While visiting the (fictional) Ventana nuclear power plant outside Los Angeles, television news reporter Kimberly Wells (Fonda), her cameraman Richard Adams (Douglas) and their soundman Hector Salas witness the plant going through an emergency shutdown (SCRAM). Shift Supervisor Jack Godell (Lemmon) notices an unusual vibration while grabbing his cup of coffee which he had set down. He then finds that a gauge is misreading and that the coolant is dangerously low (he thought it was overflowing). The crew manages to bring the reactor under control and can be seen celebrating and expressing relief.
In 1988, following a 400% increase in crime, the United States Government has evacuated Manhattan and turned the island into a giant maximum-security prison in which all inmates serve a life sentence. A 50-foot (15 m) containment wall surrounds the island and routes out of Manhattan have been dismantled or mined. Armed helicopters patrol the rivers and harbor.
In 2199, after five years of attacks by an alien race known as Gamilas, the Earth Defense Force launches a counter-offensive near Mars. The fleet's weapons are no match for the Gamilas, who easily wipe out much of the force. During the battle, EDF captain Mamoru Kodai volunteers to use his damaged ship, the destroyer Yukikaze, as a shield to cover Captain Jyuzo Okita's ship, allowing his escape. Mamoru's ship is destroyed.
Volcanic eruptions and earthquakes shake Japan. Firestorms burn beautiful Japanese cities to the ground. A weather survey group discovers that the Japanese Archipelago is moving towards the Japanese Trench, which if left to continue on its collision course, would bring the whole island of Japan under the sea.
On 16 July 1988, an orb of light destroys Tokyo and World War III begins. Thirty-one years later, in the city of Neo-Tokyo, Shotaro Kaneda has his bōsōzoku gang, the Capsules, battle their rival gang, the Clowns. While there, Kaneda's best friend, Tetsuo Shima, crashes his motorcycle into Takashi, an esper with psychic powers, who had fled from a secret government laboratory with help from a covert operative. Colonel Shikishima, assisted by another esper called Maseru, has Takashi escorted back to his original lodgings and Tetsuo is abducted. When Kaneda and his gang are interrogated, he encounters Kei, a member of the revolutionary group, and arranges her release along with the Capsules.