In 1970, former Navy SEAL John Kelly, who recently lost his pregnant wife, Patricia, in a car accident, picks up a hitchhiker named Pam on his way to his home on Battery Island in the Chesapeake Bay. They quickly become lovers, and over time Kelly discovers her full name, Pamela Madden, and that she is a runaway who became a drug mule and prostitute; she has recently escaped from her drug-dealer/pimp Henry Tucker. Kelly, along with the help of doctors Sam and Sarah Rosen, helps rehabilitate her from barbiturates. Weeks after recovering, Kelly and Pam go to Baltimore for follow-up treatment. Kelly takes them scouting through the neighborhood where her pimps work. One of them recognizes Pam and pursues them in a car chase. Kelly is gravely wounded by a shotgun blast, while Pam is recaptured and later tortured, gang-raped, and killed.

In Vietnam, a U.S. target drone (specified in the book as a buffalo hunter) discovers Air Force Colonel Robin Zacharias as a prisoner of war in a secret camp administered by the NVA. Since Zacharias possesses highly classified knowledge and has been declared killed in action, Admiral Dutch Maxwell arranges a secret rescue mission for him as well as other American POWs held in the camp. Unbeknownst to them, Soviet colonel Nikolay Grishanov has been interrogating the prisoners; he later lobbies his government to transport Zacharias and his fellow prisoners into the Soviet Union, citing their intelligence value. However, friction between the Soviets and the North Vietnamese leads the latter to decide to kill the POWs.

Meanwhile, Kelly recovers from his wounds with the help of Dr. Rosen and his head nurse, Sandra "Sandy" O'Toole. Vowing to exact revenge on the people responsible for Pam's death, he wages a private war on Tucker's drug ring, eliminating some of its players and saving some female drug mules in the process. He recruits Rosen and O'Toole to help rehabilitate one of the rescued prostitutes, Doris Brown. He later obtains more information on the drug ring from brutally torturing one of Pam's pimps, William Grayson, using a pressure chamber designed to simulate deep-water diving conditions; he is then left to die from severe decompression sickness. However, his specialized tactics, including advanced close-quarters combat, camouflaging himself as a homeless man, meticulous intelligence gathering, and manufacturing of suppressors for his firearms draw the attention of local investigators, particularly Emmet Ryan, who investigated Kelly's initial altercation and Pam's subsequent death.

Later, Kelly is approached by Admiral Maxwell to act as the pathfinder for the rescue mission on Zacharias and other American POWs, since he is familiar with the area from his days in the UDT and had previously gone behind enemy lines to rescue Maxwell's son. Kelly pauses his personal vendetta, and proceeds to Vietnam. A KGB mole informs the Soviets of the rescue mission, compromising it. However, Kelly manages to capture Grishanov while escaping from the camp, who is then used as leverage to negotiate the transfer of Colonel Zacharias and his fellow prisoners to the Hanoi Hilton, where they will be confirmed as alive and eventually returned.

Upon returning from Vietnam, Kelly finds out that Doris and her father Raymond had been killed and continues his mission. He finds out that the heroin processed by Tucker's drug ring was smuggled into the U.S. through the corpses of dead American soldiers, and also deduces that a corrupt police officer is on Tucker's payroll. Meanwhile, the CIA try to recruit him following his actions in Vietnam, and due to Kelly's difficult position, they agree to help him escape his legal troubles in return for the assassination of the mole who had jeopardized the Vietnam operation. Kelly forces the supposed mole, an aide to the Special Assistant to the National Security Advisor, to kill himself, inadvertently leaving the real mole, a Senate aide and anti-war activist, active. He then rushes to complete his vendetta, finally killing Tucker and his remaining cohorts. Corrupt police Lieutenant Mark Charon is incidentally murdered by the criminals.

Ryan deduces that Kelly is the vigilante targeting drug dealers and their corrupt police partners. He confronts him on his boat, where Kelly confesses. He bargains with the detective for one more hour of liberty before being arrested; Ryan agrees, but Kelly fakes his death by capsizing his boat. He is then rescued by his CIA superiors, who recruit him under his new identity as John Clark. He quietly resumes contact with O'Toole and marries her. Three years later, Zacharias and his fellow POWs are released after the end of the American involvement in the Vietnam War.