Hi the reason for your confusion is that nobody knows the answer - not yet, and perhaps not for another century to come. Imagine ancient Greece, and someone asking Plato what matter is made of, what particles are responsible for the elements and HOW they do that!
The only thing that we are pretty sure of, is that "empty space" isn't a true void: even when it's empty of matter it's not completely empty. But whatever particles or stuff there is that we cannot see, it certainly affects the natural size and shape of objects as well as the frequency at which clocks tick. And somehow it also makes that objects gravitate towards each other...
Einstein (1920) put it like this (compressed and slightly rephrased for simplicity):
"[Our measurement tools] are partly conditioned by the matter existing outside of the territory under consideration. This .. variability of the .. relations of the standards of space and time, or, perhaps, the recognition of the fact that ''empty space'' in its physical relation is neither homogeneous nor isotropic .., has, I think, finally disposed of the view that space is physically empty.
The ether of ..general..relativity is a medium which is itself devoid of all mechanical and kinematical qualities.. [The state of] the ether ... is at every place determined by connections with the matter and the state of the ether in neighbouring places ..".
Now we only need a super microscope