Dark matter
lol, no.
Empty space is at it says it's empty space a Vacuum if you may, no Atom just space (space is an entity) actually.
As for the empty space in an Atom, Atoms are them selfs composed of subatomic particals, Electron, Neutron and Protons, which are them self composed of Quarks, Bosons ect ect according to the standard model, the reference of empty space in atom, is the huge distance (in the atomic scale of course) between there particles in the normal state of matter.
To explain in simple terms, take the example of a sponge, a sponge has a certain volume right? but if you look at it you see that it is filled with holes with no plastic in them, if you compress the sponge to compensate for the holes in it you'll get the real quantity and volume of plastic in that state.
(if you understood don't read beyond this it might confuse you even more)
So to understand the huge amount of empty space inside an atom, we can look at exotic state of matter in the Univers, and lets take the example of the sponge again, to compress matter you need huge forces! an Example would Star cores where gravity applies such forces on matter and the energy from nuclear fusion counter that force, but what happens when there is no more fuel in the star for nuclear fusion, well gravity wins, and depending on the weight of the star the matter get compressed intel a force counter gravity, example a star like the Sun once it full is done, it core will compress to a white dwarf a white dwarf is about the size of earth yet it weighs the same as the sun (for reference the sun is millions of times bigger than earth in normal state) and the the force that prevent furthur compression is called the electron degeneracy, if the Star is heavier than the sun like 20 times the mass of the sun of the sun, the force Gravity goes beyond electron degeneracy pressure, and it manage to fuse Proton and Electrons to make neutrons, and you'll end up (with a huge bang called a supernova) and a Neutron star, to put into perspective a Neutron Star weighs from 1.5 to 3 times the Mass of the sun (if it goes beyond that it will become some else and the force that's stop it from going any further is neutron degeneracy pressure) with a diameter of a dozen of kms, to put into perspective, a spoon of neutron star matter is weighs the same as much as the Everest mountains Yup that's the amount of empty space you have in matter in normal state, and of course if the Star is heavier than 40 times than the Sun, you end up with the ultimate state of matter, (gravity wins) you end up with a stellar blackhole (and an even bigger bang a Hypernova) ....
As for empty space
According to Quantum Mechanics and new theories, there is no such thing as empty as elementary practicals of matter and antimatter appears and instantly disappears in space but that's beyond what you need to know for now.