To properly evaluate the scientific validity of sequence stratigraphy and its applicability to geologic research within the context of a Biblical worldview requires a basic understanding of the philosophy of science. A review of the philosophy of science, emphasizing its application to geology, was presented in Part I. The principles developed in Part I are now applied to stratigraphy in general. In particular, the "mixed question" problem and effects of disparate worldviews on stratigraphic method and practice are examined. In Part III, principles developed in Parts I and II will be extended to the growing field of sequence stratigraphy.