A joint operation between American and Russian Special Forces leads to the capture of General Ivan Radek (Jürgen Prochnow), the dictator of a rogue terrorist regime in Kazakhstan that had possession of stolen Soviet nuclear weapons. Three weeks later, President of the United States James Marshall (Harrison Ford) is invited to Moscow for a diplomatic dinner, during which he praises the capture and insists the United States will never negotiate with terrorists. Marshall and his entourage, including his wife Grace (Wendy Crewson) and daughter Alice (Liesel Matthews), and several of his Cabinet and advisers, prepare to return to the United States on Air Force One. In addition, a number of press corps have been invited aboard.
Former Army Ranger Cameron Poe is sentenced to prison for manslaughter for using excessive force on a drunk man while trying to protect his pregnant wife Tricia. Poe is paroled eight years later, and is to be released after being flown to Alabama on the Jailbird, a C-123K transport prison aircraft. Along with Poe are several other prisoners including his diabetic cellmate and friend Mike "Baby-O" O'Dell, who is being transferred (but not yet paroled) with Poe. The transfer is being overseen by U.S. Marshal Vince Larkin, as the transfer includes notorious criminal mastermind Cyrus "Cyrus The Virus" Grissom, gangster and Black Guerrilla member Nathan "Diamond Dog" Jones and mass murderer William "Billy Bedlam" Bedford for their transfer to a new Supermax prison. Larkin is approached at the last minute by DEA agents Duncan Malloy and Willie Sims, who ask for Sims to be brought aboard disguised as a prisoner so that he can extract more information from drug lord Francisco Cindino, a prisoner that is to be picked up at Carson City, Nevada en route. Larkin agrees, unaware that Malloy has hidden a gun on Sims' body.
Kyle Pratt (Jodie Foster), a U.S. aircraft engineer employed in Berlin, Germany, is widowed with a six-year-old daughter Julia (Marlene Lawston) after her husband David (John Benjamin Hickey) falls off the roof of their building to his death. Kyle decides to bury him in their hometown back in the U.S., on Long Island, NY. They fly aboard a passenger aircraft, the engines of which Kyle helped design. After falling asleep, Kyle wakes to find that Julia is missing. She begins to panic, and Captain Marcus Rich (Sean Bean) is forced to conduct a search. None of the passengers remember seeing her daughter, Julia has no register in either the Berlin airport or the passenger manifest, and Kyle cannot find Julia's boarding pass. Marcus and the other crew members suspect that Kyle has become unhinged by her husband's death, and has imagined bringing her daughter aboard. One flight attendant Stephanie (Kate Beahan) is particularly unsympathetic. Faced with the crew's growing skepticism regarding her daughter's existence, Kyle becomes more and more desperate. Because of her increasingly erratic, panicked behavior, air marshal Gene Carson (Peter Sarsgaard) is ordered to guard and handcuff her.
An alcoholic air marshal named Bill Marks boards a Boeing 767 non-stop flight from New York City to London. He sits next to passenger Jen Summers with whom he engages in friendly conversations. After take-off, he receives a text message on his secure phone stating that someone will die every 20 minutes unless $150 million is transferred to a specific bank account. Marks breaks protocol and consults with Jack Hammond, the other air marshal, who concludes that the threat is not valid. Marks however consults the help of Summers and flight attendant Nancy to monitor the security cameras while texting the mysterious person in order to locate him. However, Hammond is texted by the unknown person who says that he knows what is in Hammond's briefcase. As Marks confronts Hammond in the rear lavatory, the latter is revealed to be smuggling cocaine in a brief-case. Hammond attacks Marks, who responds in self-defense and breaks Hammond's neck. This incident happens exactly at the 20-minute mark.
Richard Phillips (Tom Hanks) takes command of the MV Maersk Alabama, an unarmed container ship from the Port of Salalah in Oman, with orders to sail through the Gulf of Aden to Mombasa, Kenya. Wary of pirate activity off the coast of the Horn of Africa, he and First Officer Shane Murphy (Michael Chernus) order strict security precautions on the vessel and carry out practice drills. During a drill, the vessel is chased by Somali pirates in two skiffs, and Phillips calls for help. Knowing that the pirates are listening to radio traffic, he pretends to call a warship, requesting immediate air support. One skiff turns around in response, and the other – manned by four heavily armed pirates led by Abduwali Muse (Barkhad Abdi) – loses engine power trying to steer through the Maersk Alabama 's wake.
Alex Shaw is on a motorcycle chase after a vehicle with stolen goods. He eventually catches the driver of the vehicle, but his girlfriend Annie runs into him during her driving test. She finds out that Alex is on the SWAT team after he lied and told her he was a beach cop. As an apology, Alex surprises her with a Caribbean cruise on Seabourn Legend.
On September 11, 2001, Port Authority Police officers John McLoughlin and Will Jimeno are patrolling the Port Authority Bus Terminal in Midtown Manhattan when they see a plane fly dangerously low overhead. As all of the police officers return to the station, they see on TV that the North Tower of the World Trade Center has been hit by the plane. Sergeant McLoughlin assigns many of the officers to assist in a precautionary evacuation attempt of the North Tower and they board a Metropolitan Transit Authority bus. On the bus, they hear reports that the South Tower is also hit by another plane. When they arrive at the World Trade Center, they realize the extent of the disaster, and see one of the victims jump out of the towers to certain death. The men proceed to get safety equipment from Building 5 and enter the concourse between the towers.
The battleship USS Missouri (BB-63) arrives at Pearl Harbor, where George H. W. Bush announces that the ship will be decommissioned in California, making the trip her final voyage. Casey Ryback (Steven Seagal), a Chief Petty Officer assigned as a cook, is preparing meals in celebration of the birthday of Captain Adams (Patrick O'Neal), against the orders of Commander Krill (Gary Busey), who is having food and entertainment brought by helicopter.
A man calling himself Ryder hijacks Pelham 123, a New York City Subway 6 train that departed from Pelham Bay Park station at 1:23 p.m. Ryder is accompanied by three other heavily armed men; Bashkim, Emri, and former train operator Phil Ramos. They uncouple the front car from the rest of the train and take the passengers hostage. MTA employee Walter Garber is working the Rail Control Center as a train dispatcher and receives a ransom call from Ryder, who demands $10 million in cash be paid within 60 minutes. Ryder warns that every minute past the deadline they force him to wait, he will execute a hostage.
In 2003, Maya, a young U.S. Central Intelligence Agency officer, has spent her entire brief career, since graduating from college and being recruited for the agency, focused solely on gathering intelligence related to Osama bin Laden, leader of al-Qaeda, following the terrorist organization's attack on the United States in 2001. She is reassigned to the U.S. embassy in Pakistan to work with a fellow officer, Dan. During the first months of her assignment, Maya often accompanies Dan to a black site for his continuing interrogation of Ammar al-Baluchi, a detainee with suspected links to several of the hijackers in the September 11 attacks. Dan subjects the detainee to approved interrogation techniques, i.e., stress positions, hooding, subjection to deafening noise, sleep deprivation, waterboarding, and humiliation. After failing to get al-Baluchi to give up information on an attack in Saudi Arabia, he and Maya eventually trick Ammar into divulging that an old acquaintance, who is using the alias Abu Ahmed al-Kuwaiti, is working as a personal courier for bin Laden. Other detainees corroborate this, with some claiming Abu Ahmed delivers messages between bin Laden and a man known as Abu Faraj al-Libbi. In 2005, Abu Faraj is apprehended by the CIA and local police in Pakistan. Maya is allowed to interrogate him, but he continues to deny knowing a courier with such a name. Maya interprets this as an attempt by Faraj to conceal the importance of Abu Ahmed.
Lieutenant Colonel Austin Travis leads an unsuccessful raid on a Chechen mafia safe house in Italy by a U.S. Army Special Forces team to recover a stolen Soviet nerve agent, DZ-5. One of his men is killed during the raid.
The movie begins by suggesting that friends and political allies of George W. Bush at Fox News Channel tilted the election of 2000 by prematurely declaring Bush the winner. It then suggests the handling of the voting controversy in Florida constituted election fraud.
While serving in the United States Army Special Forces in 2007, John Tyree (Channing Tatum), a Staff Sergeant, is lying on the ground after being shot multiple times in the neck and body, with his comrades gathered around him. In a voiceover, he recalls a childhood trip to the U.S. Mint and compares himself to a coin in the United States Military before stating that the last thing he thought of before he blacked out was "you".
Casey Ryback has retired from the United States Navy and is a chef at the Mile High Cafe in Denver, Colorado. Casey is taking his estranged niece Sarah to Los Angeles to visit the grave of Sarah's father. Sarah and Casey board the Grand Continental, a train traveling from Denver to Los Angeles through the Rocky Mountains. Armed mercenaries, led by former U.S. government computer hacker and computer genius Travis Dane and mercenary leader Marcus Penn, hijack the train. Dane worked on Grazer One, a top-secret military satellite particle weapon designed to destroy underground targets. The military fired Dane because of his mental instability; Dane later faked his suicide.
The film begins with commentary by passenger Detective Graham Waters (Don Cheadle) having suffered a car accident with his partner Ria (Jennifer Esposito). He mentions that the denizens of Los Angeles have lost their "sense of touch." Ria and the driver of the other car, Kim Lee, exchange racially charged insults. When Waters exits the car, he arrives at a police investigation crime scene concerning the discovery of "a dead kid."