The Orphan Master’s Son is the story of Jun Do, an “everyman” caught up in high-stakes politics in a fictionalized version of the Democratic People’s Republic of Korea. As the son of the orphan master, Jun Do grows up among orphans and bears a martyr’s name, experiences which follow him throughout his life.

During a period of national famine, Jun Do and the orphans are sent to join the army. As the head of an orphan unit, Jun Do patrols the tunnels of the demilitarized zone and learns to fight in the dark. One day, he is given a new mission: to become part of a crew that sneaks onto Japanese soil to kidnap civilians. His most notorious case is the kidnapping of a famous opera singer, after which he stops one of his comrades from defecting. As a reward, he is sent to language school, where he learns to transcribe English.

His next assignment is as a listener onboard the Junma, a fishing vessel. He intercepts signals from passing ships—an illegal act in the eyes of democratic nations. The loneliness that marked Jun Do’s childhood is eased when he finds camaraderie among the crew. He is fascinated by the signals he receives, including the transmissions of two American girls who are rowing around the world. After the Junma is boarded by American soldiers and Jun Do’s position as listener is threatened, the Captain tattoos Jun Do’s chest with the face of Sun Moon, North Korea’s national actress, to make him more convincing as a sailor. When the Second Mate defects, the crew must invent a story to save their own necks, and the Captain suggests that Jun Do sacrifice his arm to a shark in order to lend their story authenticity. An interrogator beats him mercilessly to verify his story, and afterwards Jun Do spends time recovering from his wounds in the Second Mate’s wife’s apartment.

His next mission is a summons to fly to the United States as a national hero, and it is here that he first meets Comrade Buc. The North Korean contingent lands in Texas, where negotiations to return a radiation detector fail. However, Jun Do makes a valuable contact in Wanda, an American who gives him a satellite camera that will transmit images to her phone. The Americans also give him a puppy, which he passes off to Comrade Buc to give his neighbor, the actress Sun Moon. Knowing their mission was unsuccessful, the returning North Koreans invent a story to tell their interrogators. Although the men assigned to debrief Jun Do tell him that his story has been verified, he is tricked into entering a prison camp with two medics. Once there, he befriends Mongnan, a mysterious woman who helps him survive his time in the prison. At this point, the man named Jun Do officially ceases to exist.

Months later, a man claiming to be Commander Ga is brought to Division 42, an underground interrogation center. It is believed that this man has killed Sun Moon and her children and is impersonating the real commander, a man known for his taekwondo expertise, his friendship with the Dear Leader Kim Jong Il, his marriage to Sun Moon, and his reputation for ridding the army of homosexuals. The story then splinters into three perspectives—the interrogator in Division 42 who is trying to construct a biography of Commander Ga, the imposter Ga (formerly Jun Do) remembering the events of his recent past, and the national broadcast, which spins the unfolding tragedy into a story that flatters the Dear Leader.

The new Ga’s story begins when he kills the real Commander Ga in a prison mine, after the commander attempts to sexually assault another prisoner, supposedly to teach a lesson about homosexuality. Trading his prison clothes for Ga’s uniform, the new Ga leaves the prison and travels to Pyongyang. He arrives at the commander’s house, telling Sun Moon that he has killed her husband and is taking his place. Sun Moon is incredulous and disbelieving, and at first she forces the new Ga to live in the tunnel beneath their house. Eventually, seeing he is not the cruel man her husband was, she permits him to come inside, but forbids him to touch her or to learn the children’s names. The Dear Leader summons the new Ga into his circle of confidants in anticipation of an American visit as Ga (Jun Do) is one of only a few people in the country who has been to America. Ga is in a dangerous position in the leader’s company; the leader knows he is an imposter and can easily dispose of him. But the North Koreans now have something the Americans want—a captured citizen, one of the two female rowers that Jun Do used to listen to on the Junma—and the time is right to trade her for the radiation detector.

As the Americans’ visit approaches, Ga wins the trust of Sun Moon and begins to plot an escape for her, the children, and himself. He enlists the help of Comrade Buc, the next door neighbor whom the real Commander Ga once attacked, attempting to rape him. On the day of the Americans’ visit, the female rower and the radiation detector are exchanged, and then chaos breaks out when a dog, a gift from the Americans, attacks one of the North Korean officers. Sun Moon and her children are smuggled aboard the American plane, but when the Dear Leader learns of this betrayal, Ga and Buc must pay the ultimate price.

Under intense questioning by interrogators, the new Ga refuses to confess to harming Sun Moon. This impresses the interrogator, who is horrified by the increasingly violent actions of his colleagues, the Pubyok, and whose blind, elderly parents have become frightened of him. When the imposter Ga refuses to confess anything of use, a friend of the Dear Leader removes the tattoo of Sun Moon from his chest with a box cutter, and the new Ga is sentenced to be publicly branded the following day. This is the end of an era for Ga’s interrogator, who never has the chance to finish Ga’s biography. At home, he feeds his parents a can of poisoned peaches that belonged to Comrade Buc. When he returns to Division 42, the interrogator hooks Ga up to the “autopilot,” a torture device that dispenses volts of electricity, and then hooks himself up as well. He plans to lose enough brain function to forget his identify but still be a viable member of society, perhaps living on a community farm. Ga takes control of the machine and commits suicide with a lethal dose of electricity.

The final word in the novel belongs to the official national broadcast, which reports that Ga had a change of heart after attempting to betray the Dear Leader. Desperate to get Sun Moon back, he latches onto the wing of the American’s plane and writes messages on the window in his blood for Sun Moon to see. Eventually, spotting an American aircraft carrier in the Pacific, he jumps to his death. The story of the orphan master’s son/Jun Do/Commander Ga/the nameless prisoner is turned into a propaganda piece, and after his death he is recognized as a hero and a martyr.