What is in empty space?
Empty space is comprised of quark and gluon field fluctuations.
An atom is mostly empty space, but empty space isn't really empty space. The reason it looks empty is because electrons and photons don't interact with whats there, which is quark and gluon field fluctuations.
Quantum Chromodynamics is the theory of fundamental particles called quarks. Quarks are the building blocks of protons and neutrons, and how they interact with each other through gluons. Empty space is filled with this stuff.