Science and philosophy both express, and attempt to quench, the distinctively human thirst for knowledge. Today, their mutual relationship has become one of conflict or indifference rather than cooperation. At the same time, scientists and philosophers alike have moved away from at least some of our ordinary beliefs. But what can scientific and philosophical theories tell us about the world, in isolation from each other? And to what extent does a sophisticated investigation into the nature of things force us to question commonsense beliefs? This book defends a form of naturalism which preserves the autonomy of metaphysics - the part of philosophy that aims to uncover the fundamental features of reality - while also keeping science centre stage. The proposed methodological perspective allows one to seek the right equilibrium between science, metaphysics and common sense. This is illustrated via three case studies, which provide a clear discussion of key philosophical issues.