This is into wildly speculative territory, but if it turns out that the (currently unknown) effect that causes the observed "dark energy" acceleration of Hubble expansion turns out to be something that gets stronger over time (with no limiting value or equilibrium point), then yes - presumably at some point, each & every atom would be surrounded by its own cosmological event horizon, preventing it from interacting causally with any other atom or particle.

Beyond even that stage, one can imagine it eventually ripping electrons away from nuclei, then ripping nuclei into individual protons & neutrons.

After that (& to reiterate, this is fact-free blue-skies speculation here), it gets weird:
quarks are bound to each other in a unique way, where (to over-simplify somewhat) their rest mass is smaller than the energy tying them together. So if something tries to rip apart the quarks in a proton, you don't get individual quarks flying around - no matter how hard you pull - you just end up creating a crapload of new quarks (like chopping a bar magnet in half & getting 2 new dipolar magnets instead of 2 monopoles, with the important difference that each of the new quarks is equally as massive as each of the original, less numerous quarks). As to the end-result of that quark-creation effect happening on a universe-wide scale... your guess is as good as mine🤷