At the beginning of the novel, the priest is waiting for a boat that will take him out of the capital city. He is on the run from the police because religion has been outlawed in his state and he is the last remaining clergyman. While talking to a man named Mr. Tench, he is summoned to a dying woman's house and misses his boat. He hides out in a barn on the estate of a plantation owner, befriending the owner's daughter. Forced to move on, he heads to a village in which he used to live and work as pastor. There he meets Maria, a woman with whom he has had a brief affair, and Brigida, his illegitimate daughter. He spends the night in the town and wakes before dawn to say mass for the villagers. The lieutenant—a sworn enemy of all r eligion—arrives at the end of mass, leading a group of policemen in search of the priest, and the priest goes out to the town square to face his enemy. No one in the village turns him in, however, and the lieutenant does not realize that he has foun d the man he is looking for. Instead, the lieutenant takes a hostage, whom he says he will execute if he finds that the villagers have been lying to him about the whereabouts of the wanted man.
The priest heads to the town of Carmen, and on the way he meets a man known simply as the mestizo. Uninvited, the mestizo accompanies the priest on his journey, and it very soon becomes clear that he is an untrustworthy figure, and most likely interes ted in following the priest so that he can turn him in and collect the reward money. The priest finally admits that he is, indeed, a priest. But the mestizo, who has become feverish by the second day of their journey together, does not have the strength t o follow the priest when he veers off course. The priest knows that if he enters Carmen he will surely be captured, and he lets the mestizo ride on towards the town by himself.
The priest then backtracks to the capital city. He is in disguise, wearing a drill suit, and he tries to procure a bottle of wine so he can say mass. He meets a beggar who takes him to a hotel and introduces him to a man who says he can supply him with th e wine. The man arrives and sells the priest a bottle of wine and a bottle of brandy. But, taking advantage of the priest's offer to share a drink with him, the man proceeds to drink the entire bottle of wine, thwarting the priest's plan. The priest then leaves the hotel but is caught with the bottle of brandy by a state official. After a lengthy chase through the streets of the town, during which the priest unsuccessfully attempts to take refuge at the house of Padre Jose, he is caught and taken to j ail. In jail he speaks with the prisoners, admitting to them that he is a priest. A pious woman, in jail for having religious articles in her home, argues with the priest. The next day, the priest is ordered to clean out the cells and, while doing so, meets the mestizo again. But the mestizo decides not to turn the priest in to the authorities. The priest has another face-to-face encounter with the lieutenant, but again goes unrecognized, and is allowed to go free.
The priest spends a night at the abandoned estate of the Fellows and then moves on to an abandoned village. He meets an Indian woman whose son has been shot and killed by the gringo, an American outlaw who is also on the run from police. He accompanie s the woman to a burial ground and then leaves her there. Fatigued, and almost completely drained of the will to live, the priest staggers on, eventually coming upon a man named Mr. Lehr who informs him that he is out of danger, having crossed the bor der into a neighboring state where religion is not outlawed.
After spending a few days at the home of Mr. Lehr, the priest prepares to leave for Las Casas. But before he can depart, the mestizo arrives, informing him that the gringo has been mortally wounded by the police and is asking for someone to come and hear his confession. The priest, aware that he is walking into a trap, finally agrees to accompany the mestizo back across the border. There he meets the gringo, who refuses to repent for his sins and then dies. Then, as expected, the lieutenant arrives and ta kes the priest into custody. The two men have a long conversation about their beliefs and then, when the storm front clears, the lieutenant takes the priest back to the capital city for his trial.
On the night before the priest is to be executed, the lieutenant goes to the home of Padre Jose to see if he will come and hear the confession of the captured priest. Padre Jose refuses and the lieutenant returns to the police station with a bottle of bra ndy for the priest. That night, the priest tries to repent for his sins, but finds he cannot. He wakes up the next morning afraid of the impending execution.
The next day, Mr. Tench watches the execution from the window of the jefe's office. Later that night the boy hears about what happened to the priest and realizes that the man is a martyr and a hero. He dreams about him that night, and wakes up to the sound of knocking at the door. Opening the door, he finds a man seeking shelter, and when the boy learns that the man is a priest, he swings the door wide open to let him in.