There is general agreement that physical entities exist, but there is widespread disagreement on whether nonphysical entities such as emergent quantities, mental constructs, and agencies qualify as existence and the nature of those quantities. At the core of this disagreement lie subjective worldviews and ideological convictions rather than objective reasoning based on observations. Further, there is a growing tendency to view all nonphysical quantities as properties of organization and label them emergent qualities which appear out of nothing and disappear into nothingness. In this paper we present plausible arguments that emergent qualities are not limited to large assemblies of matter and that they are encountered even at subatomic level. We also make a distinction among different kinds of nonphysical entities such as mental constructs invented by the mind and entities discovered by inference, such as the laws of nature. Finally, we present a novel view of the notion of agency, such as the agency of physics which is comprised of the laws and forces of physics, characterized by causal power with the capacity to subjugate and manipulate physical entities made of matter–energy. Once the emergent quantities, mental constructs, and agencies are properly characterized and their concealed interconnections revealed, we can develop a better understanding of reality and envisage how physical and nonphysical entities interplay and how they can be manipulated.