Instead of discussing the Black Death, what happens when a person looks past the subject matter of the book to analyze the construction of the book instead? What they find is a fascinating discussion of truth. Truth is an abstract concept which is different in many ways than fact, and in fact often times discussions which solely focus of factual knowledge miss the deeper truth that can be seen. In this case, truth is attained through a dual approach to narrative, half factual (historical fact) and half personal.
The fictional aspect of the book comes from Master John's personal life, and that fictitious aspect allows more truth to be included, because the facts of the Black Death are rooted in a personal narrative about one man's experience. The fact that the protagonist is a minister allows a natural conversation between the Plague and theodicy. Theodicy is the philosophical practice of justifying human suffering to the potential existence of a loving and almighty God. That is literally Master John's role in his community, helping his parish to understand God's love as they suffer and die in horrible confusion.
Of course Master John is also subject to horror and death, so as he attempts to navigate the fictional aspects of this story, John Hatcher's own authorial voice can be seen in the background, using this fascinating thought experiment for philosophical considerations of human suffering. This is also a major conundrum in the Humanities, because human suffering seems to add tension and value to human experience, but on the face plagues like the Black Death seem horrific and dour. How could a loving God allow terror and sickness to afflict his children? The struggle to understand this points to transcendental religious considerations.