Substance theory is a part of Ontology, the study of "what is," and focuses on the state of any object as it exists in the real world. A key part of substance theory is that it separates "the object" from "the object's properties." In this theory, something that has properties is not an object because of those properties, but because it exists regardless of them. The classic example is water, which has different properties in its different states; evaporated water is lighter-than-air and invisible, while frozen water is lighter-than-water but solid and unchanging. The "substance" of the water, however, does not change through its state changes, and so the "water" itself must be separated from its properties, as it can hold different properties at different times.
Simply put, an object is and is distinct from its properties; it can contain properties, but those properties are separately defined from the thing itself. The object exists, and its properties exist, but they are not inextricably tied together. Substance theory, at least in regards to the innate "being" of matter and energy, is supported by the Laws of Thermodynamics, which state that matter and energy cannot be created or destroyed, only shifted from state-to-state; this allows an object to be regardless of its properties at that specific moment.