Fiction and fact
The relationship between fact and fiction comes together for an experience of truth which is more than the sum of its parts (which is situationally ironic). The irony more precisely is this: Why does fiction make fact seem more true to a reader than just reading about history in a textbook? The answer is in the title: by making the story Personal the History is more native to the reader's imagination. It is a little like a language translation where John Hatcher is translating historical and scientific data into a story which is more easily "digested" by the reader.
The role of minister
Master John is an ironic protagonist for this story because the role of a minister is to support the community, but in times like these that role is essentially a martyrdom (martyr is Greek for "witness"; a martyr is someone who is called to suffer through witnessing something). In this case, he is a martyr for the tragedy of human suffering because he is unable to save the people he loves, nor can he encourage them completely, because chances are that they might get sick and die. Why shouldn't they be scared of fate? Why shouldn't they be angry with God? The minister is in a no-win situation which allows the reader to empathize with the community.
The depth of human suffering
Dramatic irony shapes the historical novel in this way: As the people begin to suffer sickness and death, their attention becomes naturally focused on death, but the levels of suffering that they end up reaching are way beyond the scope of their imagination. The most pure expression of this irony would be torture, because that is an intentional affliction of suffering which is naturally more painful and extreme than humans can fathom. The Black Plague has elements of torture in it, but it is not "caused" by anyone per say. That is, unless you accept the religious beliefs of the church in which case the suffering is allowed by the God who created everything. The depth of suffering is severe to the point of irony.
The love of God
As mentioned, the natural dramatic irony of this story is found in the perplexing sorrow and suffering of the disease and the deaths that it causes, but in addition to that dramatic irony, there is also situational irony: Because Master John is a minister of the church, he is literally obligated to defend the religion which means preaching the love of God to a community of sick and dying people. That situational irony has the makings of theodicy, especially when the protagonist has time to think and contemplate his own opinion.
The strangeness of human death
Death itself is offered as the central irony of this book. The theodicy aspect of the book drags the reader into situations and arguments that treat the issue of human suffering, symbolized by the extreme case of the Black Death. But if that sickness did not lead to death, would it matter? If no one died, then occasional sickness of any kind would be tolerable. It is death which makes this book tragic. That is ironic in many ways, but the most pressing irony is that during times of peace humans are allowed to forget about death which makes death dramatic again.
