In 1923 Tennessee, two young boys, Rafe McCawley (Jesse James) and Danny Walker (Reiley McClendon), play together in the back of an old biplane, pretending to be soldiers fighting the Germans in World War I. After Rafe's father lands his biplane and leaves, Rafe and Danny climb into the plane and Rafe accidentally starts it, giving the boys their first experience at flight. Soon afterward, Danny's father (William Fichtner) comes to take him home. He calls Rafe a "stupid boy" and beats Danny. In an effort to protect Danny, Rafe hits Danny's father with an old propeller and calls him a "dirty German". Danny's father reacts by saying he fought the Germans in the trenches in France during World War I, and that he prays that no one will ever have to see the things he saw.
On July 20, 1969, astronaut Jim Lovell hosts a party, where guests watch on television as Neil Armstrong takes his first steps on the Moon during Apollo 11. After the party, Lovell, who had orbited the Moon on Apollo 8, tells his wife Marilyn that he intends to walk on the Moon's surface.
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.
In 1993, following the ousting of the central government and start of a civil war, a major United Nations military operation in Somalia is authorized with a peacekeeping mandate. After the bulk of the peacekeepers are withdrawn, the Mogadishu-based militia loyal to Mohamed Farrah Aidid have declared war on the remaining UN personnel. In response, U.S. Army Rangers, Delta Force counter-terrorist operators, and 160th SOAR aviators are deployed to Mogadishu to capture Aidid, who has proclaimed himself president of the country.
In 1957 Brooklyn, New York, Rudolf Abel retrieves a secret message from a park bench and reads it just before FBI agents burst into his rented room. He prevents discovery of the message, but other evidence in the room leads to his arrest and prosecution as a Soviet spy.
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.
Airline pilot captain Whip Whitaker (Washington) uses cocaine to wake up after a night of very little sleep in his Orlando hotel room. He pilots SouthJet Flight 227 to Atlanta which experiences severe turbulence at takeoff. Copilot Ken Evans (Geraghty) takes over while Whip discreetly mixes vodka in his orange juice and takes a nap. He is jolted awake as the plane goes into a steep dive. Unable to regain control, Whip is forced to make a controlled crash landing in an open field and loses consciousness on impact.
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.
Chicago is paralyzed by a snowstorm affecting Lincoln International Airport. A Trans Global Airlines (TGA) Boeing 707 flight crew misjudge their turn off of Runway 29 on to the taxiway, becoming stuck in the snow and closing Runway 29, forcing airport manager Mel Bakersfield (Burt Lancaster) to work overtime. This causes tension with his wife, Cindy (Dana Wynter). Divorce is looming as he nurtures a closer relationship with a co-worker, TGA customer relations agent Tanya Livingston (Jean Seberg). Bakersfield's brother-in-law, Vernon Demarest (Dean Martin), is a TGA captain scheduled to be the checkride captain for TGA to evaluate Captain Anson Harris (Barry Nelson) during TGA's Flight 2 to Rome. Flight 2 is aboard TGA's flagship service craft, a Boeing 707 known as The Golden Argosy. Although Demarest is married to Bakersfield's sister, Sarah (Barbara Hale), he is secretly having an affair with Gwen Meighen (Jacqueline Bisset), chief stewardess on Flight 2, who informs him before the flight that she is pregnant with his child.
In the final stages of the Bosnian War in December 1995, United States Navy flight officer Lieutenant Chris Burnett (Owen Wilson) and pilot Lieutenant Jeremy Stackhouse (Gabriel Macht), who are stationed on an aircraft carrier in the Adriatic Sea, are assigned a reconnaissance mission by their commanding officer, Admiral Reigart (Gene Hackman). The mission goes smoothly until they spot suspicious activity in the demilitarized zone where NATO aircraft and the warring factions are prohibited from engaging in military activity. Burnett persuades Stackhouse to fly their F/A-18 Hornet off-course to get a close look and photograph the target. They are unaware that they photographed mass graves, and Serb soldiers see the jet. The local Bosnian Serb paramilitary commander, General Miroslav Lokar (modelled on Arkan and his Tiger militia, and played by Olek Krupa), is conducting a secret genocidal campaign against the local Bosniak population. Not wanting the mass graves to be discovered, Lokar orders the jet be shot down.
On the morning of September 11, 2001, four al-Qaeda terrorists Ziad Jarrah, Saeed al-Ghamdi, Ahmed al-Nami, and Ahmed al-Haznawi pray in their respective hotel rooms before arriving at Newark Liberty International Airport. The quartet wait at a gate after getting through security to board San Francisco-bound United 93. After 40 minutes of delay due to traffic the plane takes off, flown by captain Jason Dahl and first officer Leroy Homer, with all four terrorists on board.