Set in the height of the Cold War in the 1980s, the story begins at the Soviet Northern Fleet base in Murmansk. The 60-year-old Captain Marko Ramius sets sail aboard the Soviet Union's newest Typhoon-class ballistic missile submarine, the Red October. Equipped with a revolutionary silent drive system, the massive boat slips into the cold Arctic ocean without leaving a trace. However, Ramius is not on a standard training exercise; disillusioned with the Soviet regime, he and his key officers intend to defect to the United States and hand over the deadly submarine.

To conceal his true intentions, Ramius sends a letter to Soviet high command announcing his defection, triggering a massive naval hunt as Moscow dispatches its fleet, including an Alfa-class hunter-killer submarine commanded by Ramius's former student, Captain Tupolev, to destroy the Red October. Meanwhile in Langley, Virginia, you, a CIA analyst, examine satellite imagery, signal intelligence, and personnel files to deduce Ramius's true motives. You realize he does not intend to launch a nuclear strike, but rather to defect. CIA Director Admiral Greer sends you to convince the Americans to help Ramius, placing you aboard the US attack submarine USS Dallas, commanded by Captain Bart Mancuso. After you present your evidence, Mancuso agrees to aid the defection.

Far at sea, Ramius stages a fake catastrophic reactor failure aboard his submarine, forcing the loyal crew to evacuate into rescue vessels. Left behind with his trusted co-conspirators, Ramius prepares to deliver the vessel. However, a GRU saboteur disguised as a cook remains hidden on board. The cook opens fire, fatally wounding First Officer Vasily Borodin and taking Ramius hostage at gunpoint in a narrow passageway. Lacking combat training and completely unarmed, you find yourself on board the Red October hundreds of meters beneath the surface, facing the gunman with the outcome of the Cold War hanging on your next action.