Let's say that I have a box which is 100% empty.
I fly into the vacuum of space, open the box and close it after a certain time.
Then I go back to earth and my question is..
What's in my box? (particles/atoms/molecules?)
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How big is your box?
Where do you open the box?
As the link to wikipedia says:
the interstellar medium is extremely dilute by terrestrial standards. In cool, dense regions of the ISM, matter is primarily in molecular form, and reaches number densities of 10^6 molecules cm−3. In hot, diffuse regions of the ISM, matter is primarily ionized, and the density may be as low as 10^−4 ions cm−3. Compare this with a number density of roughly 10^22 cm−3 for liquid water. By mass, 99% of the ISM is gas in any form, and 1% is dust. Of the gas in the ISM, 89% of atoms are hydrogen and 9% are helium, with 2% of atoms being elements heavier than hydrogen or helium
You could have a wildly varying amount of "stuff" in your box. And are you talking only baryonic matter? Because there are many, many things that can be considered "stuff" in the universe, which may already have been in your box.
My friend Steve (Larian) answers a similar question here: How vacuous is intergalactic space?
It depends where in the "vacuum of space" that you open the box. You will find comparatively much matter inside the solar system, and considerably less in the interstellar medium. Though even in the ISM there are huge hydrogen clouds just waiting to form stars. Once you get outside the galaxy, though, you will probably be lucky to catch even a single atom.
According to this even in the region between galaxies, there would probably still be a few protons/Hydrogen atoms per cubic meter. Since baryonic matter is at most 4.5% of the energy density of the universe, your cubic meter box would have at least 20 times as much energy density in the form of dark matter and dark energy. Of course the walls of your box could stop the protons/Hydrogen atoms from escaping, but the dark matter and dark energy would freely flow through the walls. But that is OK since the would also flow into your box as fast as they escape. In fact they were already there while you were still on earth.