How something decays depends on what it is. The main thing is to keep track of all the conservation laws, and to always decay into less massive things. For instance, there’s something called baryon number which seems to be conserved, and protons are the smallest baryons, so a proton seems to be unable to decay. On the other hand, current theories suggest that baryon number might not be absolute, and that protons can decay, just not very easily. In this case, you’d get a positron, to conserve charge, and one or more photons, to carry off the rest of the energy. The positron, on the other hand (or, equivalently, an electron) can’t decay on its own, because charge is an absolute conservation law, and there’s no charged particles lighter than the electron/positron. The only way to get rid of electrons and positrons is to annihilate them with each other to produce a couple of photons: There’s zero net charge before, and zero net charge after. The photon can’t be gotten rid of at all, permanently, since it’s massless.
So, assuming that the proton decays (because that’s more interesting), let’s look at the ultimate fate of the Universe: Evenetually (after hundreds of billions of years), all the protons decay, and therefore so do all normal atoms (since you can’t have a nucleus without protons). Any neutrons left over from those atoms decay to a proton + electron + antineutrino fairly quickly (about 15 minutes, which is an eternity as particle physics goes, but an eyeblink in cosmology), and the protons formed this way will eventually themselves decay. The neutrinoes left over from this process don’t decay because they’re the lightest spin 1/2 particle, so they stick around, too (it’s possible to convert a neutrino and an antineutrino into a pair of photons, but highly unlikely). Now, most of the positrons produced from proton decay will end up annihilating with electrons, but there’ll be a few electrons and positrons left over that are too far apart to meet (and getting farther apart yet, as the Universe continues to expand). However, the electromagnetic force, like gravity, has an infinite range, so they’ll still interact, if very weakly, across the many light-years. An electron and a positron interacting in this way form what’s called a positronium “atom” (even though there’s no “nucleus”, per se), and there’s no upper limit on how far apart the two particles can be and still interact this way, so atoms billions of light-years across are not out of the question. Aside from those positronium atoms, the only other other particles left will be photons and neutrinoes.
Just because there’s (almost) nothing but light left in the Universe doesn’t mean that it’ll be a very bright place. Even today, photons outnumber all of the heavy particles (heavier than neutrinoes) combined, and the night sky is what most folks would call dark. In the far-distant future, there’ll be a factor of two or three more photons, but they’ll be spread out over a far greater area. Some science fiction writers have supposed that a new Big Bang might arise from the emptiness, but so far as I know, that’s nothing but science fiction: No current theories support that possibility.