The protagonist of the story, the priest is waging a war on two fronts: haunted by his sinful past, he struggles internally with deep qualms about himself, and pursued by the authorities, he works to evade capture by the police for as long as he can. The priest is not a conventional hero: he is at times cowardly, self-interested, suspicious, and pleasure-oriented. That is to say he is human. The extraordinary hardships he has endured on the run from the government for eight years have transformed him into a much more resilient and mentally strong individual, although he still carries around with him strong feelings of guilt and worthlessness. He is self-critical almost to a fault.
What is remarkable about Greene's depiction of this person is that he refuses to spare us the priest's less-than-noble side, and yet also convincingly shows him overcoming his weaknesses and performing acts of great heroism. The most important single act comes near the end of the novel, when he decides to accompany the mestizo back across the border, to the state in which he is being hunted, in order to hear the confession of a dying man. The priest does not recognize the real value of his actions, nor does he fully comprehend what kind of impact he has had on people's lives. He tends to hear only from those people who have been hurt or disappointed by him in some way: Maria, Brigida, the pious woman. He does not see the many people whose lives have been touched merely by coming into contact with him or hearing about his death; Mr. Tench and the boy are the two most notable examples. Because this positive influence remains hidden to him, the priest does not have a true conception of the value of his life, and therefore, remains an extremely humble man to the day of his death. He also feels that he can never be truly penitent for his sexual relationship with Maria, since it produced Brigida, his daughter, whom he loves very deeply.
Driven by an obsessive hatred for the Catholic Church, the lieutenant will stop at nothing to apprehend and execute the priest, who, he believes, is the last remaining clergyman in the state. The lieutenant is a principled, disciplined man with a strong sense of justice. He is committed to political ideals that he thinks will help the poor and create equality and tolerance in the state. Unfortunately, he oftentimes allows his focus on his noble goal to obscure questions about the means he is employing to reach that goal. The most striking example of this is his decision to round up hostages and execute people if the villagers lie to him about the priest's whereabouts. As we see, the selection process is entirely arbitrary, hardly just, and extremely violent. It is easy to see why the people are as skeptical of the state as they are of the church. But even this person is capable of change. From time to time throughout the novel he shows that he is not an unkind person. After his conversation with the captured priest, he softens considerably, trying to find someone to hear the priest's confession and bringing him a bottle of brandy to quiet his fears. The political movement to which he belongs has taught him to look at people in generalized terms: that is, all priests are bad and all those working for the lieutenant's cause are good. The priest, who proves himself to be modest, intelligent and compassionate, disrupts the lieutenant's habitual way of looking at the Catholic clergy. By the end of the novel, he has accomplished his mission, but he feels a strange sense of emptiness and despondency. Without a target, his life has no meaning or sense of purpose and Greene suggests that lingering doubts fill the lieutenant's mind troubling him about whether he has done the right thing by killing the priest.
The mestizo, who functions as a "Judas" figure of the novel, appears at significant points throughout the priest's journey. The irony is that although he means the priest nothing but harm, he actually provides opportunities for the priest to commit heroic acts. It begins with the small sacrifice after the two first meet: the priest refuses to abandon the mestizo when he falls ill, finally putting him on the back of a mule and sending him towards a town. When the mestizo tracks him down on the other side of the border, the trap he has set becomes an opportunity for the priest to turn away from the life of leisure, and recommit himself to his ideals and his duties. The mestizo, always interested in getting something for nothing, asks the captured priest to pray for him. The priest tells him that forgiveness cannot be given out, but must be worked for, and that he had better do some true soul-searching if he is concerned about the sins he has committed. The mestizo is in many ways the mirror image of the priest: the priest has done this soul-searching but despairs over having no third-party to hear his confession. But, while the priest attempts to root out all self-interested motivations from his mind, the mestizo is concerned only with his own advantage. Nevertheless, the priest's actions towards the mestizo make the mestizo a sympathetic character.