Vaisheshika portrays the world as a mind-independent reality grounded in eternal, indivisible atoms and a set of basic ontological categories. At the most fundamental level, all gross physical substances are composed of atoms of earth, water, fire, and air, each possessing its own inherent nature and specific qualities. These atoms are partless, indestructible, and distinguished from one another by particularity, which ensures that even the smallest units of reality are genuinely many. The physical elements are only one subset of substances, however; ether, time, space, self, and mind are also counted as real substances that provide the conditions for experience, location, duration, and cognition. Reality is thus articulated through substances, their qualities, and their motions, all bound together by universals, particularities, and the relation of inherence.

The emergence of the perceptible world is explained through the combination and separation of atoms. Single atoms, which are not directly perceptible, first join to form dyads, then triads, and progressively larger aggregates that become the familiar objects of everyday experience. Different configurations and motions of these atomic groupings give rise to the diversity of forms and properties observed in the world, so that a pot, a body, or a flame is nothing more than a specific arrangement of elemental atoms bearing particular qualities. Change, growth, and destruction are understood as reconfigurations of these atomic groupings, with dissolution returning atoms to more basic combinations. The properties of composite objects depend on the natures and arrangements of their constituent atoms, and these properties inhere inseparably in the substances that bear them.

To render this world intelligible, Vaisheshika also appeals to a subtle causal order that includes both physical and moral dimensions. Motion and interaction among atoms do not occur at random but are governed by causal laws and by an unseen factor, linked with merit and demerit, that helps account for the ordered unfolding of events and the cycles of creation and dissolution. Within this framework, selves and minds are not illusory but real substances that encounter the atomic world through the senses, one object at a time, within the vast fields of space and time. The result is a rigorously realist vision: a universe of enduring atomic and non-atomic substances, structured by categories and relations, whose lawful combinations and transformations manifest as the rich tapestry of physical phenomena.