A massive metal ring with engraved cover stones is discovered in the sands of Giza, Egypt in 1928, by an archaeologist named Langford and his young daughter, Catherine. Many years later, the elderly Catherine Langford offers Egyptologist and linguist Daniel Jackson the chance to translate the Egyptian hieroglyphs on the cover stones. Jackson accepts and travels to a US Air Force installation where he examines the stones. Special Operations Colonel Jack O'Neil arrives to take command of the project and he declares it "classified" before Jackson can begin his research.
The film begins at Flemner Air Base 20 years prior. A pilot named Leland "Buzz" Harley (Bill Irwin) loses control of his plane and ejects, leaving his co-pilot Dominic "Mailman" Farnum (Ryan Stiles) to crash alone; although Mailman survives, he's mistaken for a deer owing to the branches stuck to his helmet and is shot by a hunter. Topper Harley (Charlie Sheen) wakes up from a nightmare he's having about the event when Lt. Commander Block (Kevin Dunn) asks him to return to active duty as a pilot in the U.S. Navy, to help on a new top secret mission: Operation Sleepy Weasel.
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 After the bulk of the peacekeepers are withdrawn, the Mogadishu-based militia loyal to Mohamed Farrah Aidid have declared war on the remaining UN personnel.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.
Ryan Bingham (George Clooney) makes his living traveling to workplaces around the United States and breaking the news to workers that they have been let go for employers unwilling to do it themselves. Ryan also delivers motivational speeches, using the analogy "What's In Your Backpack?" to extoll the virtues of a life free of burdensome relationships with people as well as things. Ryan relishes his perpetual travels. His personal ambition is to become only the seventh person to earn ten million frequent flyer miles with American Airlines. While traveling, he meets another frequent flyer named Alex (Vera Farmiga) and they begin a casual relationship.
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.
Robin Monroe, a New York journalist working for Dazzle, a fashion magazine, is invited by her boyfriend Frank to spend a week holidaying with him on the island paradise of Makatea, in the South Pacific. The final leg of their journey to Makatea is in a small dilapidated aircraft, piloted by middle-aged American Quinn Norris. They are accompanied by Quinn's girlfriend and co-pilot Angelica.
The film opens showing Louis "Louie" Zamperini flying as a bombardier of a United States Army Air Forces B-24 Liberator bomber, during an April 1943 bombing mission against the Japanese-held island of Nauru. The plane is badly damaged in combat, with a number of the crew injured. The hydraulics of the plane are shot and damaged, but the pilot, Phil, manages to bring it to a stop at the end of the runway thanks to a flat tire.
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.
Since winning the Wings Around the Globe race in the first film, Dusty Crophopper has a successful career as a racer. Unfortunately, his engine's gearbox becomes damaged due to being regularly forced over its limits. With that particular model of gearbox now out of production and none available anywhere, Dusty's mechanic Dottie fits a warning light to his control panel to ensure he doesn't damage his gearbox any further. No longer able to race and faced with the possibility of returning to his old job as a crop-duster, Dusty goes on a defiant flight and tests his limits. In doing so, Dusty exceeds his limits and makes a forced landing at Propwash Junction airport, causing a fire.
Major Vic "Deak" Deakins (John Travolta) and Captain Riley Hale (Christian Slater) are pilots in the United States Air Force. After a sparring match, the pilots are assigned to a top secret evening exercise over Utah, flying a B-3 Stealth Bomber (a fictional iteration of the B-2 Spirit stealth bomber) with two B83 nuclear bombs on board.
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.
In 1939, Captain Daniel McCormick (Mel Gibson) is a United States Army Air Corps test pilot. After a successful run and subsequent crash landing in a prototype North American B-25 Mitchell bomber at Alexander Field in Northern California, McCormick is greeted by his longtime friend, Harry Finley (George Wendt) who's a scientist. Finley confides that his latest experiment, "Project B", has succeeded in doing the impossible. The machine, built by Finley and his team of scientists, is a prototype chamber for cryonic freezing. When McCormick's girlfriend, Helen (Isabel Glasser) goes into a coma from an accident and the doctors doubt she will ever recover, McCormick insists he be put in suspended animation for one year, starting November 26, 1939, so he will not have to watch Helen die.
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.