With those three particles, they can only be still relative to a frame of reference. That fact is not removed by isolating them. As far as I can tell, exactly the same thing would happen if you made those three particles still to each other, inside the container or out. The state of the rest of the universe does not impact those three particles relationship to one another, since we have pre-defined their relationship as being identical in either case.
The only possible exception, which I mentioned above, is when the entire universe becomes still. No frame of reference containing motion. If the universe were just three particles, or anything else, I have no idea what would happen. Simply isolating three particles, or having a universe consisting of solely three particles, does not incur that situation though. There will still be frames of reference that contain motion, even if those particles are stationary relative to each other. Those frames could be moving in the space between the particles, for example.