The United States nuclear strategic missile submarine USS Alabama is given the mission to go on patrol and be available to launch its missiles in a pre-emptive strike if the Russian nuclear installation attempts to fuel its missiles. Captain Frank Ramsey (Hackman) is the commanding officer of the sub, one of the very few Captains remaining in the U.S. Navy with any experience in combat. He chooses as his new executive officer (XO) Lieutenant Commander Ron Hunter (Washington), who has an extensive education in military history and tactics, but no combat experience.
The Alabama eventually receives an order to launch its missiles on the Russian nuclear installation, based on satellite information that the missiles are being fueled. Before the Alabama can launch its missiles, a second message begins to come through, but it is interrupted by the attack of a Russian Akula-class attack submarine friendly to the ultranationalist cause. Too deep for communications, attacked by the hostile Akula and with an order in hand to launch, Captain Ramsey decides to proceed with the launch. XO Hunter refuses to concur as is procedurally required to launch, and instead tries to confirm the second message, which he believes is possibly a retraction of the previous launch order. As the command crisis escalates, Ramsey portrays the XO as an upstart Harvard graduate who does not respect his place in the chain of command.
Eventually, Hunter orders the arrest of Ramsey for attempting to exceed his authority. While Hunter is attempting to confirm the second launch message, the Russian Akula-class reappears. The Russian sub is destroyed, but the Alabama is damaged heavily. The ship's communications are knocked out, several crew members are killed, and the boat takes on water, nearly sinking past the "crush depth" limit at which the submarine's hull will collapse. While Hunter waits for communications to be restored, officers loyal to the captain leave the conn together. Ramsey escapes confinement with their help to confront Hunter with charges of mutiny, placing the XO and officers who assisted him under arrest.
Ramsey nearly succeeds in launching the missiles, prevented only when Hunter persuades the weapons officer to stall for time while he re-takes the bridge with his officers. In the end, a standoff ensues. The conflicted officers agree to wait until the last possible moment to launch the missiles. The communications equipment is repaired in time and it is revealed that the Russian army has the situation under control and the rebellion is subdued, eliminating the need to launch the missiles.
The movie culminates in a review at the Pacific Fleet headquarters in Hawaii where several admirals express grave concern about the breakdown of nuclear launch operations in wartime. While the elder Ramsey voluntarily retires, and the young Hunter is recommended for a command by Ramsey, the movie aims to present the intractably uncertain nature of the launch scenario, in essence placing full blame on neither character. A gentlemen’s reconciliation between officers occurs at the closure of the film.
Russian ultranationalist leader Vladimir Radchenko denounced the pressure from the U.S. as an act of war. Radchenko also denounced the Russian President as a U.S. puppet and called for all Russian people to join him in revolt. On October 18, the Russian Parliament was suspended and martial law was declared as a result of riots and revolts. On the next day, Radchenko and Russian rebel forces seized a region around Vladivostok. The region housed a naval base and a nuclear missile base with Russian ICBMs. Russian Forces began to seize the Radchenko-controlled areas. American, British and French forces went on a state of high alert.
On October 20, Radchenko threatened nuclear attacks against the United States, Japan and anyone who would move in on rebel forces. The American President set all U.S. forces to DEFCON 4. On October 26, Radchenko stole the launch codes for his ICBMs from the Russian government. U.S. forces went to DEFCON 3. However, on November 1, Radchenko and his forces surrendered to the Russian forces, ending the short-lived civil war. The war ended with fewer than 100 deaths of Russian soldiers.
Although the film does not claim to be based on a true story, events that transpire throughout the plot are strikingly similar to one of the most tense periods of the Cuban Missile Crisis, only the roles of the Americans and Soviets are reversed. On October 27, 1962, a Soviet submarine officer named Vasili Alexandrovich Arkhipov had convinced his captain not to launch a nuclear-tipped torpedo while trapped by a group of U.S. warships near Cuba.