Set during the tense times of the Cold War, the daring defection of a top level Soviet submarine captain puts the whole world in danger. Jack Ryan, a CIA specialist, is called in to analyze the situation and help the United States (US) government avoid a military conflict that would disturb the balance of peace between the US and the Soviet Union (USSR). An intense exploration of the problematic peace between the two world powers, the novel keeps the reader in suspense as people at all levels, both military and civilian, race to avert a global nuclear crisis.

Captain Marko Ramius commands the Soviet flagship submarine, the Red October. Motivated by his wife's death due to Soviet incompetence, Ramius and his top officers plan to defect to the US. Ramius kills the political officer on board and tells the crew that their mission involves absolutely zero radio contact. The officers fool the crew with a fake radiation scare so that they will be ready and willing to leave the submarine when it is time to defect.

Ramius sends a letter to the Soviet Navy, informing them of his plans to defect. The Soviets send out all of their ships and submarines out to look for the Red October. This provokes the American and British militaries because of so many submarines and ships in the Atlantic Ocean. The American President meets with the Soviet ambassador, who claims that it is a rescue mission. The Americans offer to assist in the rescue mission as a way to stay in control of the situation. The American and Soviet naval vessels come to many close calls as they meet each other in the Atlantic. Jack Ryan, newly arrived from England, tells the President that the Red October is planning to defect. He advises the president to offer the defectors asylum.

One of the submarines that is chasing the Red October strains its engines and sinks. One sailor survives. While that sailor is being treated in a US Naval Hospital, the Soviets are worried that he will wake up and reveal that he is from the Red October. When he does wake up, he reveals he is from a different submarine, therefore letting both the Soviets and the Americans know that there is more than one missing submarine and that the Red October is still at large.

Skip Tyler develops a secret plan to take possession of the Red October while allowing the crew to return to the Soviet Union. They use a deep-sea rescue vehicle to take the crew off the submarine. Then they blow up a decoy submarine and tell the Soviets that the Red October was destroyed. The top officers of the Red October pilot the submarine to a secret port in the US. After they are safely in port, the officers, including Captain Ramius, are given new identities in the US while their submarine, the Red October, is analyzed by US military intelligence. Jack Ryan returns home to his family in England and the US avoids a military conflict with the USSR.