The final assumption of ontological philosophy is the method it uses to decide which of the possible ontologies to believe, and here it departs from epistemological philosophy by adopting the empirical method, rather than the rational method of traditional philosophy.

The empirical method is basically an inference to the best explanation of what is found in the natural world, and though this method presupposes the validity of explanations of some kind, its standard of which is best can be used with various kinds of explanations.

The best explanation, the one it is rational to believe, is the one that explains the most with the least, that is, which explains the greatest range of effects with the fewest and simplest causes.

The scope of an explanation is the range of phenomena that it can explain as effects, and since an explanation that explains more effects is better, the empirical method requires us to prefer the explanation with the largest scope, other things being equal.

The simplest explanation is the one that uses the least in the way of causes, and so when different explanations cover the same range of effects, it is rational to prefer the one that uses the fewest and/or simplest causes.

An inference to the best explanation is relative to the kind of explanation being sought, and there are at least three different kinds of explanations with which the empirical method can be used to discover what is true. One is the basic kind used in natural science. Another kind is distinctive of the social sciences and humanities. And the third is the kind used by ontological philosophy.

Natural science typically infers to the best efficient-cause explanation. Efficient-cause explanations explain what happens in the world by citing the conditions that bring it about and laws of nature that link those conditions to events of the kind being explained.

The scope of an efficient-cause explanation is the range of phenomena that can be explained in that way. A measure of its scope is the range of phenomena covered by the relevant laws of nature or the range of effects that can be explained by the same cause (or same kind of cause).

Since laws of nature are what connect efficient causes with their effects, the simplest efficient-cause explanations is usually the one that cites the fewest laws of nature and/or the simplest laws of nature to explain what happens.

One ontological explanation is simpler than another when it uses fewer kinds of ontological causes or when the causes it uses are themselves simpler (for example, substances with temporally simple rather than temporally complex essential natures).

A rational-cause explanation is an explanation of the behavior or beliefs of subjective beings like ourselves by appeal to the desires, beliefs, perceptions and the like that are responsible for them. In this case, the "law of nature" connecting cause (or reason) and effect is our own capacity to reason deployed under the relevant conditions. However, rational explanations do not reliably lead to agreement about which causes (reasons) are responsible for beliefs or behavior.

The validity of ontological-cause explanations is the second assumption of ontological philosophy. The empirical method in ontology requires us to believe the best ontological-cause explanation of the natural world. Such an inference to the best ontological-cause explanation is the method that will be used to establish the ontology that will be used to show what holds necessarily in our world. Its foundation, in other words, is empirical ontology.

The scope of an ontological explanation is the whole world. But one ontology can still have a larger scope than another. It has a larger scope when it explains some aspects of the world that the other merely assumes. Or when it shows something to be necessary which they other takes to be merely contingent.

In ancient (epistemological) philosophy, Plato and Aristotle assumed that we know by a kind of intuition in which the objects of knowledge are present to us. Thus, they distinguished between perceivable objects in the natural world and rational objects which they thought had a radically different nature. The rational objects were supposed to explain the natures of the perceived objects.

The rational method in medieval philosophy was basically a matter of mustering arguments for the existence of a transcendent God, and since God is supposed to have created the world, that meant using what we know about the natural world to prove the existence of something outside space and time.

The rational method is the method that philosophy has traditionally used to decide what to believe about the world. Epistemological philosophy takes as its foundation an explanation of the nature of reason that is based on reflection. Though such a theory might also be considered an inference to the best explanation, it is not primarily an explanation of the behavior and beliefs of subjective beings in the natural world, but rather an explanation of what we know about how we know from reflecting on ourselves. Philosophers in different eras had different theories about the nature of reason.

The rational method of modern philosophy was fundamentally different from ancient and medieval philosophy because it had given up naive realism about perception and recognized that our experience of the world is mediated by ideas in the mind. But that basic theory about the nature of reason took various forms, with different way of proving necessary truths about the natural world. For example, Descartes argued that clear and distinct ideas reveal the nature and existence of the external world, whereas Kant argued that certain propositions about the world must hold because they are prior to experience (that is, synthetic a priori propositions).

In the contemporary period, Anglo-American analytic philosophy tried out a new theory about the nature of reason derived from reflection on our use of a public language. It took various forms, from ideal language philosophy and logical positivism (which took the meanings and references of some words for granted) to ordinary language philosophy and naturalized epistemology (which tried to explain meaning and reference empirically). But the only truths that could be shown to be necessary were analytic truths.