By layers I mean;
Perhaps, something might be there very deeper in the empty-space that we can't see.
For example: Some atoms, or molecules are really small. So small, in fact, that it's impossible to see one with the naked eye, or even with the most powerful of microscopes.
We don't know, if there is anything. We know that most is in fact made up from nothing, as far as I understand. Even in an atom if you look at a classic illustration:
The neutrons and electrons etc. are orbiting the nucleus, but most of the atom is empty space.
For instance this one:
A hydrogen atom is about 99.9999999999996% empty space.
If that is not what you mean, then you have the dark matter and energy, whichever it is. That the scientists believe exists, because the mass of the galaxies doesn't add up at all, so there is a lot that is unaccounted for so to speak. And can't remember if the expansion of the Universe is also related to this. But they believe that DM/DE doesn't interact with us or something, which is why it is so difficult to figure out. if I understood it correctly.
The two most outstanding unsolved problems of modern cosmology today are the problems of dark energy and dark matter. Together these two problems imply that about a whopping 96% of the energy content of the universe is simply unaccounted for within the reigning paradigm of modern cosmology.
So they are working on different ways to figuring it out.
But again, can't stress enough that I might misunderstand most, if not all of it. So don't take it as being the absolute truth!!