In a coherent conception of reality, physics and metaphysics should both come together to create a comprehensible worldview. This was the case in the Newtonian picture of reality which turned out to be limited at the beginning of the 20th century. The quest for a new synthesis, a more reliable picture of reality incorporating current theories and observations, has not been fulfilled in spite of a hundred years of interpretive discussions. The claim of this paper is that the missed unison can be found in Tuomo Suntola’s Dynamic Universe (DU). This exceptional theory covers the domains of the theory of relativity and quantum phenomena and fairly exceeds their level in philosophical virtues. DU is studied here from the perspective of natural philosophy concentrating on the basic principles of the theory, and the prominent metaphysical features that in addition to the mathematical structure can be found in a proper physical theory. Relying on the zero-energy principle, DU opens up a new kind of holistic framework where the Newtonian furnishings for reality are left behind. By transforming the Newtonian clockwork into a pendulating, spherically closed 4D-sphere, DU discloses a seamless connection between mass, space, motion, and energy. In this representation all the seemingly separated objects are parts of a single totality and ultimately constructed of waves. Their interrelations can be universally formulated as their state of motion does not depend on the time or the site of observation. In addition to its importance for physics, the framework provides justified answers to many age-old disputes in natural philosophy starting from the basic substance of being, the origin and reference of movement, and the possibility of empty space – the most basic questions pondered by giants like Democritus, Plato, Aristotle, Descartes, Leibniz, and Newton. Most importantly, in DU mental properties can be neatly incorporated into the physical world, and conscious activity of human beings can be befitted into the overall evolutionary scheme.