A man calling himself "Ryder" (John Travolta), along with three other heavily armed men Bashkim (Victor Gojcaj), Emri (Robert Vataj) and former train operator Phil Ramos (Luis Guzmán), take Pelham 123, a New York City Subway 6 train that had departed from Pelham Bay Park Station at 1:23 p.m, uncoupling the front car from the rest of the train and taking the passengers hostage. MTA employee Walter Garber (Denzel Washington), a former assistant chief transportation officer, is working the Rail Control Center as a train dispatcher and receives the ransom call from Ryder, who demands $10 million in cash be paid within 60 minutes, and warns that for every minute past the deadline they force Ryder to wait, he will execute a hostage.
Bashkim kills a plainclothes Transit Police officer attempting to arrest him. He and Ramos then allow all the people not in the front car to be released except for motorman Jerry Pollard (Gary Basaraba), who is one of Garber's friends. Garber reluctantly negotiates with Ryder and develops a rapport, while Ramos and Emri set up a wi-fi booster apparatus to enable Ryder internet access in the tunnel on his laptop computer. He uses it to watch the Dow Jones Industrial Average plunge nearly 1,000 points during the next hour in response to the taking.
Lieutenant Camonetti (John Turturro) of the NYPD Emergency Service Unit, also known as the Hostage Negotiation Team, enters RCC to take over negotiations and Garber is ordered by his boss to leave the premises. Even though Camonetti told Ryder that Garber's a train dispatcher, Ryder still wants him to be the negotiator. When Ryder threatens to kill the motorman, Camonetti refuses to call Garber and Ryder kills the motorman. Ryder threatens to kill another hostage if Camonetti still doesn't bring Garber back, so he is brought back in. The motorman was a friend of Garber's and Garber blames Camonetti for the motorman's death. Camonetti apologizes for the motorman's death.
Camonetti learns Garber is being investigated for allegedly accepting a $35,000 bribe to recommend a Japanese car manufacturer for the next subway car contract, thus his demotion to train dispatching. He becomes suspicious and asks Garber to consent to a search of his home. Ryder also discovers the allegations through online news reports and forces Garber to confess by threatening to kill a passenger. Garber explains he took the bribe to pay his kids' tuition, but also claims that he would have made the same decision regardless of the bribe.
The Mayor (James Gandolfini) agrees to pay Ryder's ransom demand and orders cash from the Federal Reserve to be rushed to Vanderbilt Ave and 42nd Street to be delivered. The police transport delivering the money is involved in an accident and, despite the efforts of police motorcyclists, they fail to deliver within the deadline. Garber tries to bluff and tells Ryder that the tunnel was the only thing separating him from the money, unaware that Ryder could see the outside of Grand Central Terminal via his laptop. For lying, Ryder threatens to execute one of the children hostages and the child's mother, however another hostage, who was a former US Army Air-Assault Soldier, intervenes and instead gets shot by Ryder. A short gunfight then erupts, where in a NYPD sniper is bitten by a rat and accidentally fires his gun and kills Ramos.
Based on several clues that Garber receives during the conversation, the NYPD discover that Ryder's real name is Dennis Ford, a former manager of a private equity firm, who was sentenced to 10 years in prison for investment fraud for stealing from the city pension fund. Although Ford had accepted the prosecution's 3-year plea bargain agreement, he received a sentence of 10 years from the judge. One of the Mayor's aides mentions the extreme drop in the major stock indexes, the Dow Jones Industrial Average and the Nasdaq Composite, due to the news coverage of the hostage-taking, which some in the media have suspected to be terrorism. The Mayor deduces that such an event would allow Ryder to make spectacular returns if he bet against the market that day (the ransom money not being Ryder's main objective), so he asks the SEC to identify major trades on put options.
Garber is flown to Grand Central Terminal, the closest station to the takers' location, when Ryder demands he personally deliver the ransom. Garber accepts a concealed pistol from a police officer and drops off the money. Ryder brings him aboard and orders him to operate the train to the next station, where he and the hijackers exit the train during a brief railroad switch stop. To ensure that the police follow the train (and go to a wrong place), Ryder uses a special mechanism to lock the driving lever in the full-speed position, bypassing the dead-man's switch. Per Ryder's demands, the signals have been set to green and the train speeds ahead towards Coney Island. Garber manages to separate himself from the takers at a railway crossing and then follows them as they escape to the emergency exit inside the Waldorf-Astoria Hotel. Ryder parts ways with Bashkim and Emri, who are later shot dead via suicide by cop after being surrounded by police.
The runaway train's automatic brake is tripped by an unaltered red signal one station from Coney Island and it comes to a halt safely. Police learn Ryder is not on board. Ryder hails a taxi while Garber, who gets a truck, is in close pursuit. Ryder checks his laptop and finds that his $2 million investment in gold derivatives has amassed him a $307 million profit. Ryder leaves the cab on the Manhattan Bridge amid traffic and takes the bridge's pedestrian walkway but Garber catches up to him. As Garber holds Ryder at gunpoint, Ryder says that he is not going back to prison and gives him a 10 second ultimatum to kill him, before the other NYPD officers catch up to them. As he reaches the final seconds of the countdown, Ryder pulls out his gun in a provocative gesture which forces Garber to shoot. With his dying breath, Ryder calls Garber his hero as NYPD officers arrive on scene. Afterward, the mayor thanks Garber for saving the hostages, and hints the city will support him in the bribery investigation. Garber is later seen coming home with groceries, including a half-gallon of milk he promised his wife he'd bring home during an earlier phone call.
