In the opening of Waiting for the Barbarians, the novel’s protagonist, the magistrate, faces Colonel Joll, a sinister official and member of the Empire’s new secret police, the ''Third Bureau.'' Joll and his Third Bureau believe that the barbarians are planning a coordinated attack on the frontier regions. For this reason Joll has traveled a long distance from the capital to the magistrate’s outpost. The magistrate does not buy the theory of a barbarian threat. He has been living in peace in his outpost for most of life, trading with the nomads who Joll sees as the enemy.
Joll sets out on an expedition in search of barbarians. He comes back with a group of fisher people and nomads. Although the magistrate is horrified, he turns his back and blocks his ears as Joll’s prisoners are tortured in the barracks. The magistrate argues a little with Joll about his interrogation methods and the idea that you can get truth out of people you torture. Joll ambiguously suggests that he’s after a different kind of truth than what the magistrate considers truth. It seems as though he takes pleasure in inflicting suffering.
The magistrate is unsettled by Joll’s presence. He wants to continue his peaceful life as it was before, serving his Empire in the way he always has. He doesn’t want to consider Joll’s Empire as the same as the one he serves. He avoids confronting the fact that it is. He spends days in the local inn sleeping with a small “birdlike” young woman.
Joll goes back to the capital to submit his report. The prisoners are released. When the magistrate sees them he imagines finishing them off and putting them in a mass grave. They are so broken and brutalized he can’t imagine how they can possibly return to their lives. Slowly, one by one, they leave. All but one: a blinded girl whose legs were broken at the ankles, who begs for food in the streets. The magistrate tells her she can’t be on the street. He takes her in to his room. He’s stricken by an urge to help her, to soothe her. He starts by washing her feet and her broken ankles. Soon he washes her entire body, stripping her. He doesn’t reflect on the power dynamic. He can’t explain his desire to clean her and oil her. It’s now a sexual desire. The fact that he feels no particular sexual attraction to her baffles him. He meditates at length on his sexuality and her lost beauty or hideousness—he can’t tell. He tries to see her for what she was before. He can’t get past the scars and the idea of what has been done to her. Night after night she stays in his room. He begs her to tell him what happened to her. She doesn’t want to talk about it. Again, he doesn’t reflect on his position as an interrogator. She submits to him though he doesn’t have sex with her. She finally tells him how the torturers burned out her eyes and use a two pronged fork on her body and killed her father in front of her. After she tells him, he’s repulsed by her though he doesn’t consider why. He goes back to the inn instead, to the small, “birdlike” girl who’s easy to be with. The nomad girl asks him why he rejects her but he has no answer. She gestures that she wants to be with him. Instead he puts her out of his room. He doesn’t reflect on the new phase of torture that he’s putting her through. After this, filled with confused feelings about the girl, the magistrate decides to take her back to her people. He and the girl go with two soldiers and a guide on horses on a treacherous journey into the desert regions toward the mountains. They encounter difficulties. They lose horses. They run out of water for a time. During the journey a comradely feeling rises between him and the girl. She’s more resilient than the men, and he comes to respect her. They make love. His feelings trouble him more. It seems as though he might be falling in love with her. They finally spot some nomads. They track them down. When they reach them he proposes to the girl to come back with him to the outpost. He wants her to return of her own choice. She says she doesn’t want to go back to that place. They say goodbye and she rides off with the nomads to her people.
When he gets back to the outpost a man from the Third Bureau is there, and he informs the magistrate that he is being charged with treason. He is imprisoned in the same barracks room where the barbarians were interrogated. At first he feels giddy about his imprisonment for how it puts him on the side of the girl. He conjures the spirit of the girl in that place and imagines her being tortured in disturbing detail. He feels the anguish of solitary confinement. He stinks and his body is broken. He finds a way out of his cell.
The Third Bureau sends out troops to find the enemy. The troops return with prisoners at night. The town gathers at night to watch as they torture the prisoners in public. They get children to join in, beating the men who have their hands fastened to their cheeks with wire. Joll leads the public scapegoating. He heckles the barbarians. The magistrate, freed from his cell, demands that they stop. They beat the magistrate in front of the crowd and return him to the cell. Finally Joll interrogates the magistrate. The magistrate tells Joll what he thinks of him. He is tortured, though the process is not described.
Joll heads out again with more soldiers, leaving the warrant officer, Mandel, in charge of the magistrate. The warrant officer makes a game of torturing the magistrate naked in front of townspeople. One day he puts the magistrate in a woman’s dress, ties his hands behind his back and hangs him from a tree by the wrists. The magistrate’s shoulders splinter. He’s left to hang.
He finds his way out of the tree and begins to beg in the town. At first people dismiss him, but little by little he discovers that some still respect him. Women feed him. He learns that the barbarians have flooded all the fields. People begin to pack up and leave the outpost on the long trek back to the capital. Mandel and his soldiers condemn those who leave as traitors. But more and more people pack up. They leave at night. Mandel is not to be seen as his soldiers terrorize the town. The magistrate is getting healthier. One day a soldier arrives, dead and bloated, crucified on a post on the back of a horse. At this point Mandel takes all but three soldiers and leaves.
The magistrate returns to his old room. Winter is on its way. He takes charge, encouraging people to grow root vegetables within the city walls. It seems as though the barbarians are watching the town. Everyone is waiting for them. They dig up crustaceans from around the lake and gather as much food as they can for the winter.
Late one night Joll returns in his black carriage with a couple of terrorized soldiers. They’re in a panic. They discover that Mandel has gone. The magistrate faces Joll and tells him he’s delivered evil upon himself. Then the magistrate demands one of the soldiers tell him what happened. The soldier tells him that they were lured deeper and deeper into the desert and mountains by the barbarians who were too elusive to catch. The men starved in the desert. They were picked off. They fled. They never confronted the barbarians in a battle. They were terrified. Joll and the soldiers flee at night.
The magistrate remains with a few townspeople and only three soldiers. They hunker down and wait for winter. They wait for the barbarians to attack. The first snow begins to fall. The magistrate reflects on the possibility that he lost his way a long time ago.
