On July 2, a 500 km wide alien mothership enters Earth's orbit and deploys several dozen saucer-shaped "destroyer" spacecraft, each 15 miles (24 km) wide. As they take position over some of Earth's major cities, David Levinson (Jeff Goldblum), an MIT graduate working for a cable company in New York City, discovers hidden transmissions in Earth's satellites which he realizes is a timer counting down to a coordinated attack by the aliens. With the support of his estranged wife Constance Spano (Margaret Colin), the White House Communications Director, he and his father Julius (Judd Hirsch) gain entrance into the Oval Office to notify President Thomas J. Whitmore (Bill Pullman) about the attack. Whitmore orders large-scale evacuations of the targeted cities, but the aliens attack with advanced directed-energy weapons before these can be carried out. Whitmore, portions of his staff, and the Levinsons narrowly escape aboard Air Force One as Washington, D.C. is destroyed.
Growing up in Texas, Chris Kyle is taught by his father how to shoot a rifle and hunt deer. Years later, Chris has become a rodeo cowboy and returns home to find his girlfriend in bed with a stranger. After telling her to leave, he is mulling it over with his brother when he sees news coverage of the 1998 U.S. embassy bombings and decides to enlist in the navy. There he is eventually accepted for special training, becoming a U.S. Navy SEALs sniper.
In 1954, a nuclear bomb is detonated at the moment a giant creature emerges from the ocean. In 1999, Project Monarch scientists Ishiro Serizawa and Vivienne Graham investigate a colossal skeleton unearthed in a collapsed mine in the Philippines. They find two spores; one dormant and one hatched that made a trail into the sea. In Japan, the Janjira Nuclear Power Plant experiences unusual seismic activity and Supervisor Joe Brody sends his wife Sandra and a team of technicians into the reactor. A tremor breaches the reactor, leaving Sandra and her team unable to escape while the plant collapses.
On the morning of June 6, 1944, the beginning of the Normandy Invasion, American soldiers prepare to land on Omaha Beach. They suffer heavily from their struggle against German infantry, machine gun nests, and artillery fire. Captain John H. Miller, a company commander of the 2nd Ranger Battalion, survives the initial landing and assembles a group of his Rangers to penetrate the German defenses, leading to a breakout from the beach. In Washington, D.C, at the U.S. War Department, General George Marshall is informed that three of the four brothers of the Ryan family were killed in action and that their mother is to receive all three telegrams in the same day. He learns that the fourth son, Private First Class James Francis Ryan, is a paratrooper and is missing in action somewhere in Normandy. Marshall, after reading Abraham Lincoln's Bixby letter, orders that Ryan must be found and sent home immediately.
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.
United States Naval Aviator LT Pete "Maverick" Mitchell and his Radar Intercept Officer (RIO) LTJG Nick "Goose" Bradshaw fly the F-14A Tomcat aboard USS Enterprise (CVN-65). They, with Maverick's wingman "Cougar" and his RIO "Merlin", intercept Mikoyan-Gurevich MiG-28s over the Indian Ocean. Cougar engages one of the hostile aircraft and afterwards is too shaken to land, despite being low on fuel. Maverick defies orders and assists Cougar despite also being low on fuel. Cougar gives up his Wings of Gold, citing his newborn child that he has never seen. Despite his dislike for Maverick's recklessness, CAG "Stinger" sends him and Goose—now his top crew—to attend the Top Gun school at NAS Miramar.
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.
In 2005, scientists discover an extrasolar planet, which they name Planet G, with conditions similar to Earth. In 2006 NASA transmits a powerful signal from a communications array in Hawaii. Meanwhile, slacker Alex Hopper gets arrested while attempting to impress Sam Shane, daughter of U.S. Pacific Fleet commander Admiral Terrance Shane. Stone Hopper, Alex's older brother and a naval officer, is infuriated at Alex's lack of motivation and forces Alex to also sign up and earn a commission in the U.S. Navy.
The film covers the court-martial of two U.S. Marines, Lance Corporal Harold Dawson and Private Louden Downey, who killed a fellow Marine, Private William Santiago, at the Guantanamo Bay Naval Base in Cuba. Santiago compared unfavorably to his fellow Marines, had poor relations with them, and failed to respect the chain of command in attempts at being transferred to another base. An argument evolves between base commander Colonel Nathan Jessup and his officers: while Jessup's executive officer, Lieutenant Colonel Matthew Markinson, advocates that Santiago be transferred immediately, Jessup regards this as akin to surrender and orders Santiago's commanding officer, Lieutenant Kendrick, to train Santiago to become a better Marine.
On August 12, 2011, large masses thought to be meteors land in the oceans near several major coastal cities. The objects are discovered to be spacecraft containing hostile extraterrestrial life. Marines from Camp Pendleton arrive in Los Angeles, including SSgt. Michael Nantz (Eckhart), an Iraq War veteran. Nantz was to begin retirement, but because of the attack, he is made the acting platoon sergeant for 1st Platoon, Echo Company, of the 2nd Battalion 5th Marines.
In 1984, Soviet submarine Captain First Rank Marko Ramius (Connery) commands Red October, a new Typhoon-class nuclear sub featuring a caterpillar drive, rendering it undetectable to passive sonar. Ramius leaves port on orders to conduct exercises with the V.K. Konovalov, commanded by his former student Captain Tupolev (Skarsgård). Once at sea, Ramius kills political officer Ivan Putin (Firth), and commands the crew to head toward America's east coast to conduct missile drills.
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.