Science and theology, as I have attempted to sketch out, are two similar disciplines in that they follow similar methodology. Another aspect which they share is this: both have a metaphysical foundation – without metaphysics, there can be no real science and no real theology.
For example: metaphysics are in play before any scientific/theological data is used to come to any conclusions – metaphysical presuppositions. These are ideas that you believe that you bring to the table before any scientific/theological work is done, and these form the grid or lens through which the data is interpreted.
From a theological standpoint, metaphysical assumptions include things such as what you think of the nature of God (or how you conceive of God), what you think the nature of reality is, things o that nature. These metaphysical assumptions shape the conclusions you come to in any kind of theological enterprise. Certain metaphysical assumptions lead to various theological views such as Calvinism, Thomism, Eastern Orthodoxy, and a host of other traditions.
From a more scientific standpoint, certain assumptions about, say, language shape the conclusions one can come to in the field of say, philosophy of language, philosophy of mind, cognitive sciences and even neuroscience. For example, if one holds to metaphysical realism (which roughly says that there is an objective reality apart from observance/experience of human beings, i.e, it exists objectively), one will come to very different conclusions than someone who holds metaphysical subjectivism, a viewpoint that says our only reality is our mental activity – reality does not exist apart from perception.
The point of this overly-dense post is to at least give some kind of understanding of the role of metaphysics in both science and theology as the foundation which we build off of and the lens through which were interpret our data.