The prologue of the story occurs in late 1970. John Kelly participates in an Underwater Demolition Team's destruction of an oil rig irreparably damaged by Hurricane Camille the previous year. While driving to pick him up after the job, Kelly's pregnant wife Patricia is killed in a car accident. Meanwhile, Robin Zacharias, an Air Force colonel and F-105 pilot, is shot down during a Wild Weasel strike over North Vietnam. The story moves to late spring in the first chapter.
Robin is captured and reported killed in action. He is transferred to a secret POW camp administered by the NVA. The purpose of the camp is to elicit aid from the Soviet Union. Each of the high-ranking prisoners possesses highly classified technical knowledge and has already been declared dead, allowing the Soviets to interrogate them, in exchange for support in the war. Conducting the interrogation is Colonel Nikolai Yevgenievich "Kolya" Grishanov. He is a humane man who lobbies his government to have them brought to the Soviet Union in safety, but friction between the two allies is leading the North Vietnamese to decide to kill the POWs. While Zacharias is being moved to his cell, a U.S. target drone photographs him. Admiral Dutch Maxwell recognizes the pilot, who had helped develop the Strategic Air Command's war plans. This helps Maxwell justify an operation to send Marines into North Vietnam to rescue the POWs.
Still struggling with the loss of his wife, Kelly meets a girl named Pamela Madden, who has escaped from prostitution and serving as a mule for a drug dealer named Henry Tucker. Kelly becomes romantically involved with Pam. He also befriends two doctors, Sam and Sarah Rosen, who are both professors at the Johns Hopkins University School of Medicine. With the help of the Rosens, Kelly helps Pam recover from her addiction to barbiturates. While bringing her into the city for treatment, Kelly becomes curious about her past. Unfortunately, Billy Grayson, Pam's old pimp, recognizes her and pursues the couple in a car chase. Billy manages to wound Kelly and kidnap Pam, eventually raping, torturing, and murdering her. When Kelly sees a picture of Pam's body, learns the brutal manner of her death, and discovers that the police have little interest in investigating the crime, he vows to take revenge on the people responsible. Kelly embarks on a rigorous exercise regimen to speed his recovery. Using the covert operations skills he learned in the military, he prepares to wage a private war with Tucker and his drug ring. Meanwhile, he is approached by Admiral Maxwell, who recruits him to spearhead a covert operation to free the POWs. Kelly had gone behind enemy lines near the camp to rescue Maxwell's son, and is the only person they know of who knows the area.
Kelly must now repeatedly shift gears between his private revenge project and training for his mission in Vietnam. Both plots require similar mindsets, call on similar skills, and provoke the same moral quandaries. After interrogating and murdering several members of Tucker's gang, he collects sufficient intelligence to go after one of the ringleaders, who turns out to be Billy Grayson. Kelly captures Billy, while rescuing and rehabilitating another prostitute, Doris. Doris is nursed back to health with the help of the Rosens and their head nurse Sandy O'Toole. Sandy and Kelly begin an awkward romance. Eventually, Doris is returned to her family after being admonished to tell no one what happened. After a lengthy and brutal torture session utilizing a pressure chamber to simulate deep water diving conditions, Billy provides the information needed to eliminate the rest of the gang; he is then left to die from severe decompression sickness. Before Kelly can act on this new data, he must leave for Vietnam.
Due to a KGB mole, the Soviets anticipate Kelly's arrival and the mission is disastrously compromised. However, during his escape Kelly manages to capture Grishanov. The U.S. uses Grishanov as a bargaining chip to negotiate the transfer of the POWs to the Hanoi Hilton, where they will be confirmed as alive and eventually returned. The presence of mind Kelly shows in capturing rather than killing the Soviet officer impresses the CIA officers involved in the operation, particularly since it ultimately leads to the survival of Zacharias and the other POWs.
Upon returning to the United States, Kelly learns that Doris and her father had been murdered; he quickly deduces that there is a corrupt police officer on Tucker's payroll. Meanwhile, the police investigating the murders are beginning to close in on Kelly. Kelly determines that the location of Tucker's heroin lab is on board a derelict ship. He raids the drug lab, and eliminates still more members of Tucker's gang. He also frees Xantha Matthews, another prostitute and drug mule. Kelly deduces from the formaldehyde smell of the bags containing the Asian heroin that it has been smuggled into the U.S. inside the corpses of American soldiers killed in Vietnam.
Admiral Greer and CIA official Robert Ritter attempt to recruit Kelly to join the agency; however, by this point the police are closing in on him. Ritter agrees to help Kelly escape his legal woes in return for an illegal side operation of his own. The mole has been mis-identified as an aide to the National Security Advisor. A member of the wealthy elite, he is deemed politically untouchable and so cannot be charged with treason. As Clark, Kelly kills the supposed mole, inadvertently leaving the real mole, a Senate aide and anti-war activist, in place. To identify the mole, Ritter had leaked 3 different stories to those he suspected of revealing the information. When a KGB officer informs Ritter about a certain detail in one of the leaks, he is able to deduce the source. Kelly then rushes to complete his vendetta. Tracking the last of the gang to a new drug lab, he eliminates Tucker's mafia contacts, who have killed the corrupt police officer, Lt. Mark Charon, and Tucker himself.
Emmet Ryan, the lead police investigator, has finally identified and built a case against Kelly. He confronts Kelly on his boat, where Kelly comes clean about the drug gang and his operations against it. He begs Ryan for one more hour at liberty to put his affairs in order before being arrested; Ryan agrees. Instead, Kelly uses the hour to make his final preparations and then stages a feigned escape attempt using his boat. The Coast Guard is enlisted to pursue, piloted by Kelly's close friend Quartermaster Manuel "Portagee" Oreza. Kelly is eventually run down but blows his boat up rather than allow himself to be captured. With all the loose ends tied up, Portagee and the police assume Kelly is dead and close the case. Instead, Kelly is rescued by his CIA contacts, who recruit him into the agency under the new identity of Clark. He later quietly resumes contact with Sandy and marries her. The book closes with John Clark watching the release of the POWs after the end of the war on TV as Admiral Dutch Maxwell calls Clark to congratulate him on his efforts. When Sandy asks about the caller, John replies: "A friend... From another life" implying the demise of John Kelly and his transformation into John Clark.