All of us (or at least most of us) have beliefs about what exists: the universe, time, living beings, we humans and our place within the cosmos, etc. These individual entities or concepts that we believe in, however, normally do not exist in a vacuum without interrelation. Instead, we construct systems of belief, where things fit together into a “big picture” explanation of reality. This big picture makes up our metaphysical beliefs.
As Austin Cline of About Agnosticism/Atheism explains:
“In Western philosophy, metaphysics has become the study of the fundamental nature of all reality — what is it, why is it, and how are we can understand it. Some treat metaphysics as the study of ‘higher’ reality or the ‘invisible’ nature behind everything, but that isn’t true. It is, instead, the study of all of reality, visible and invisible; and what constitutes reality, natural and supernatural.”
Many atheists often eschew metaphysics as one of those arcane subjects of philosophy, which asks pointless and untestable questions about reality. However, as Cline explains:
“Because metaphysics is technically the study of all reality, and thus whether there is any supernatural element to it at all, in truth metaphysics is probably the most fundamental subject which irreligious atheists should focus on. Our ability to understand what reality is, what it is composed of, what ‘existence’ means, etc., is fundamental to most of the disagreements between irreligious atheists and religious theists.”
One way to think about metaphysics is that, even if science (or some epistemology of the sort) informs our beliefs about what exists, metaphysics is concerned with finding a place for what exists within a broader philosophical and theoretical framework. Metaphysics is concerned with fitting the pieces together.