The archetypal priest
The priest serves as this story's protagonist which means the reader is experiencing the horror of the Black Plague through the deaths of locals to whom the minister must administer the sacraments and funerals. In other words, he is a natural choice for exploring the human experience of the plague because he serves his community as a touchstone for them and their lives, and he also serves God through representing the religion of Christianity to suffering people. This reaches an archetypal level because the dichotomy of religion and death is accentuated by the Plague (it is a naturally extreme event in human history).
The martyred support system
As a supporter of people, we see that Master John struggles to understand his own opinions and feelings in the context of his role. The duality of his character stems from the fact that he is just a normal person like everyone else, but during extreme times of duress the public need for religious support often becomes urgent and complicated. The people ask the same questions that plague John in his private life: Why would God torture and kill humans by allowing (or even causing) sickness and death? He is martyred by his commitment to service because his own emotions are set aside.
The motif of suffering
A large part of the book's artistic purpose seems to be an elaboration of suffering among the community. The basic shape of suffering stays the same, like a theme in music, but the variations on that theme provide a plenary motif that shows Master John (and the reader therefore) the true depth and confusion of human tragedy. The heaviness of fate is clear. As people die, they leave other people around them to become sick and to suffer and survive without them—while mourning the many people lost.
Dread or horror through motif
Many kinds of suffering do not involve dread or horror. For instance, running a mile will hurt for most people, but that isn't naturally horrific. However, if a person is running from a jaguar or something, then the suffering does take on the flavor of horror and dread. This story is soaked with dread, because again and again the people cry out to God in confusion for him to give them mercy, but the Plague serves as a natural symbol for merciless confusion and sorrow. Just like with the running metaphor, sickness can be suffering without horror if the sickness is not likely to lead to death, but in this community, sickness is leading to death by the score every day.
The allegory of theodicy
As an allegory, the story is an allegorical depiction of theodicy. That means that the story serves to raise ideas and concerns through situational scenes which comment artistically on theodicy. Theodicy is the philosophical name for the question this community brings to Master John. "Why would a loving a supreme creator God cause his created children to suffer and die?" This question is naturally complicated, but especially for John, since this philosophical experiment is embodied in community members whose experience of suffering John witnesses and advises.