What I find interesting in Plantinga's book, Where the Conflict Really Lies, is how he handles evolution. This is usually the area that is brought up first when someone brings up the conflict between science and theistic religions.
His approach to this problem is to distinguish between evolution as a scientific explanation and evolution with added metaphysics. With the added metaphysics one gets either the theistic guided evolution or the naturalist unguided evolution. Guided evolution is justified in this manner: God can use whatever means he wants to get us to the state we are in today. The core conclusion is that theism is not opposed to evolution (and argues specifically against claims made by Dawkins, Dennett, Paul Draper and Philip Kitcher), but to unguided evolution: (page 63)
"The scientific theory of evolution as such is not incompatible with Christian belief; what is incompatible with it is the idea that evolution, natural selection, is unguided. But that idea isn't part of evolutionary theory as such; it's instead a metaphysical or theological addition."
That resolves the issue of a conflict between theism and evolution. He addresses miracles later which I am still reading.
However, his use of this distinction between guided evolution and unguided evolution comes back later in the text. (I've skimmed ahead.) He will later present his arguments to show that guided evolution is in more harmony with science than unguided evolution which leads to irrationality.