If we were able to create a large container, of perfect vacuum, somehow isolated from all external electromagnetic and nuclear forces, and then release a particle into it at the top, then from a classical perspective, the motion of the particle is extremly simple.
It would fall downwards with an acceleration of 9.81 $ms^2$, just as every other mass would. It wouldn't fall any slower, per the definition of the experiment and our understanding of classical mechanics. It would simply accelerate downwards.
Naturally, we can't really do this experiment in real life, at least not in this form, as it is very difficult to prepare perfect vacuums completely isolated from all external forces (and measurement of individual atoms/particles is not well explained by classical mechanics). However, some experiments have come close enough to confirm that atoms fall as expected [1], and it would be weird to think that gravity mysteriously turns off when you break an atom apart into subatomic particles.
But you don't even need to do this experiment to know that atoms are affected by gravity. You can tell by the fact that you are breathing! The earth's atmosphere is made up of a large number of atoms. If they did not respond to gravity, then they would simply fly in straight lines, bounce off the earth, and eventually escape the earth's sphere of influence, never to be seen again. 343
Imagine you threw a large number of perfectly elastic bouncy balls down into a deep pit. If they were unaffected by gravity, they would simply bounce out, and keep going upwards. If they are affected by gravity, then they will bounce upwards, but eventually fall back down again, reaching a height determined by the initial kinetic energy they were given, and the strength of the gravitational field. This is a massive oversimplification, but it is broadly similar to the earth's atmosphere. The fact that molecules in our atmosphere reach heights of hundreds of kilometres before falling back is due to the fact that the force of gravity on an individual atom is very small compared to the forces of collisions with the other molecules. Never the less, they go up, and come back down, same as anything else does
1. https://news.stanford.edu/pr/99/atomgravity990825.html (Someone please let me know if they can find a reference to the original work.) 104