CIA analyst Jack Ryan attends a diplomatic conference in Moscow as part of an American delegation to the Soviet Union. He learns that the CIA's most highly placed agent, codenamed "CARDINAL", is none other than Colonel Mikhail Semyonovich Filitov, the personal aide to the Soviet Minister of Defense and a national war hero. Filitov was recruited by GRU colonel and British agent Oleg Penkovsky, and offered his services to the CIA after the deaths of his wife and two sons; the latter two were killed during their service in the Red Army. As a result, Filitov has been passing political, technical, and military intelligence to the CIA for the past thirty years.
The U.S. discovers through "National Technical Means" that the Soviets are working on an ABM defense system codenamed "Bright Star", based at Dushanbe in Tajikistan. Emilio Ortiz, a CIA liaison, is sent to aid Mujaheddin rebels in the region. One rebel leader, known as "the Archer" due to his expertise in using surface-to-air missiles to bring down Soviet ground support aircraft, is questioned after unwittingly witnessing a test of the Soviets' ABM system. The Archer determines that the Soviet installation is a threat to him and his people, and tasks his group with attacking and pillaging the facility. In the end, the guerrillas destroy a large amount of Soviet equipment. However, the rebels suffer horrendous losses, including the death of the Archer.
Ryan travels to New Mexico to meet with the country's top SDI researcher, U.S. Army Major Alan Gregory, whom he brings to Washington, D.C., to brief the president. Gregory lives with another scientist, Candi Long, who is working on adaptive optics for use in the development of laser weaponry. A lesbian KGB agent, Bea Taussig—who has unluckily fallen in love with Long—describes Gregory and his work to her KGB handler, Tanya Bisyarina. The KGB launches a plan to kidnap and debrief Gregory.
Filitov is arrested after his work for the CIA is discovered. However, Ryan concocts a plan to both secure the return of Filitov and arrange the defection of the sitting KGB chairman, Nikolay Borissovich Gerasimov. Gerasimov is angling to take over as General Secretary in the wake of Filitov's arrest, something Ryan is determined to prevent because of his unyielding anti-American ideology. Ryan schemes to go public with the prior capture of the Soviet submarine Red October , banking on the political instability of the Soviet Politburo. He plans for Filitov and Gerasimov to be exfiltrated on the American delegation's aircraft, while Gerasimov's family is extracted from Estonia by John Clark onto the submarineUSS Dallas
. He reveals this in a private meeting with Gerasimov, forcing the KGB chairman's hand.
On Gerasimov's orders, three KGB officers kidnap Gregory and hold him in a shabby desert safe house, planning to send him to Moscow for debriefing as counter-leverage should he refuse to defect and Ryan reveal the intelligence windfall, along with the nuclear missiles the U.S. received when the Red October crew defected. Their plans are foiled when the FBI sends in the Hostage Rescue Team to retrieve Gregory and return him to Long. Among those killed is Bisyarina. Ryan informs Gerasimov of the failed operation, forcing the enraged chairman to accept Ryan's defection offer. Taussig is arrested when she attempts to seduce Long after Gregory is reported kidnapped, though she'd originally only wanted to comfort her.
The flipped Gerasimov fetches Filitov from his confinement. The three make their way to Sheremetyevo Airport, awaiting the departure of the American delegation. Unfortunately, two KGB officers, Klementi Vladimirovich Vatutin, the KGB officer who had been interrogating Filitov and finally extracted a confession from him, and Sergey Nikolayevch Golovko, who would become an old, somewhat friendly acquaintance of Ryan's over the years, become aware of their planned departure. As Gerasimov and Filitov escape, Ryan allows himself to be captured by Golovko, banking on his diplomatic status to protect him from harm. Golovko then escorts Ryan to the private dacha of General Secretary Narmonov, where the two men discuss the CIA's interest in his political position and the CIA's interference in their internal security.
Ryan returns to the United States, where he and several others attend the funeral of Filitov, who had died of heart disease in the months following his CIA debriefing period. Filitov is buried at Camp David, within twenty miles of the Antietam battlefield. A Soviet military attaché attending the funeral questions why Filitov would be buried so close to American soldiers. Ryan, always working to keep the peace, explains to him, "One way or another, we all fight for what we believe in. Doesn't that give us some common ground?"