On the evening of September 11, 2012, the 11th anniversary of the September 11 attacks, a group of Islamic militants attack on the American diplomatic compound and a nearby CIA Annex in Benghazi, Libya. They kill four Americans, including a US Ambassador, J. Christopher Stevens. A security team of six members fight to defend Americans but only partially succeed.
On Saturday, December 13, 1941 at 7:01 a.m., a woman goes swimming somewhere on the California coast, only to find a Japanese submarine surfacing beneath her. The submarine crew believes they have arrived in Hollywood, and the vessel submerges while the woman swims to safety.
Criminals Robert Trench (Denzel Washington) and Michael Stigman (Mark Wahlberg) are questioned by the United States Border Patrol after a meeting with drug lord Manny "Papi" Greco (Edward James Olmos) in Mexico. Unknown to Stigman, Trench is an undercover DEA agent and reports to his superior, Jessup (Robert John Burke), that he failed to acquire cocaine from Greco that they could use as evidence to convict him.
A Senate Armed Services Committee interviews a candidate for the position of Secretary of the Navy. Senator Lillian DeHaven (Anne Bancroft) from Texas criticizes the Navy for not being gender-neutral. Behind the curtains, a deal is struck: If women compare favorably with men in a series of test cases, the military will integrate women fully into all branches of the Navy.
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.
The USS Tiger Shark is a U.S. Navy submarine on patrol in the Atlantic Ocean during World War II in August 1943. She receives orders to pick up survivors spotted adrift by a British PBY Catalina patrol plane. She retrieves three survivors – the British nurse Claire Paige (Olivia Williams) and two men, one of them wounded – from the British hospital ship Fort James, which had been sunk two days earlier; one of the survivors blames the sinking on a German U-boat that he briefly saw on the surface just before the Fort James suffered a torpedo hit. As they pick up the survivors, the crew of the Tiger Shark spots a German warship bearing down on them. The submarine has several encounters with the German warship and suffers damage from depth charges in the process. Later, the commanding officer of the Tiger Shark, Lieutenant Brice (Bruce Greenwood), discovers that the wounded survivor is actually a German prisoner-of-war, Bernard Schillings (Jonathan Hartman). Brice confronts him because he thinks Schillings has been making noises to betray the Tiger Shark 's position to the German warship. Brice shoots Schillings dead when the German panics and grabs a scalpel to defend himself.
In 1940, Canadian weapons of war including newly manufactured aircraft ordered by the British, have to be delivered to the United Kingdom. Lord Beaverbrook, head of the UK Ministry of Aircraft Production also arranged for purchase of aircraft from manufacturers in the United States. Aircraft were first transported to Dorval Airport near Montreal, and then flown to RCAF Station Gander in Newfoundland for the transatlantic flight. The initial ferry flight of seven Lockheed Hudson bombers from Gander Airport in Newfoundland took place on November 10, 1940.
In the Philippines, a terrorist kills the U.S. ambassador, his son, and dozens of children at an elementary school, using a vehicle-borne IED disguised as an ice cream truck. The mastermind, a Chechen terrorist named Abu Shabal (Jason Cottle), escapes to a training camp in Indonesia. Elsewhere in Costa Rica, two CIA operatives, Walter Ross (Nestor Serrano) and Lisa Morales (Roselyn Sánchez) meet to consolidate intelligence about their target, a drug smuggler named Mikhail "Christo" Troykovich. Christo's men kill Ross and capture Morales, who is imprisoned in a jungle compound and tortured.
Flying students Danny Collins (Johnny Downs), "Jinx" Roberts (Bobby Jordan), "Scrapper" McKay (Ward Wood) and "Zombie" Parker (William Benedict) are suspected of a series of murders perpetrated by engineer, Arthur Galt (Robert Armstrong) operating as a Nazi agent known as the Black Hangman. He has disposed of several people who accompanied him on an expedition which located lost helium deposits in Africa.
Policeman Jon Davis (Richard Arlen) informs "Foxy" Pattis (Chester Morris) at his shooting gallery, that his criminal father has died. Foxy blames all policemen, feeling they harassed him all his life and were responsible for his death. Both men enlist in the United States Army Air Forces where Foxy becomes the instructor at an aerial gunnery school. He makes life miserable for Jon, now a "Flying Sergeant" student, trying to force the former policeman to resign.
Doug Masters (Jason Gedrick), son of veteran U.S. Air Force pilot Col. Ted Masters (Tim Thomerson), is a hotshot civilian pilot, hoping to follow in his father's footsteps. Then, his hopes are dashed when he receives a notice of rejection from the Air Force Academy. Making matters worse is the news of his father being shot down and captured by the fictional Arab state of Bilya while patrolling over the Mediterranean Sea. Despite the incident occurring over international waters, the Arab state's court finds Col. Masters guilty of trespassing over their territory and sentences him to hang in three days.
While on a routine patrol on United States airspace west of Alaska, pilots Doug "Thumper" Masters and Matt "Cobra" Cooper test the g-forces of their F-16C planes. Their antics get them carried away, as they stray over Soviet airspace. As they are being escorted back into U.S. airspace, one of the Soviet planes has Doug on missile-lock. This leads to a brief dogfight. In the ensuing battle, Matt loses control of his plane and is too late to save Doug, who is shot down by the Soviets. The next day, the U.S. Secretary of Defense publicly denies the incident, claiming a training accident caused by a fuel system malfunction killed Doug. This later revealed in Iron Eagle on the Attack that Doug actually survived by ejecting before his aircraft exploded and became a POW for a few years until released on goodwill.