I have a hunch that it will be discovered (if it hasn't already been - I don't know I'm pretty sure this is probably already known even though I've never heard anybody discuss it) that given enough time all matter dissolves into energy because at some level - at least thermal - all matter is radioactive. Explanation: When light is omitted by an atom, say from the splitting of a covalent bond in the chemical reaction in the fuel on the top of a struck match, some tiny amount of matter -- a much smaller amount than in a nuclear chain reaction - is converted to the light given off. The light we see from a struck match is in fact a tiny chunk matter unwound into radiation. And because all matter gives off some level of radiation - at least thermal, some tiny amount of matter is constantly being sublimed from all atoms everywhere. Doesn't this imply that given enough time all matter will dissolve into light? That eventually, barring some strange type of death, the universe will be truly empty - no matter anywhere, no APPRECIABLE light anywhere. Also don't bring up black holes as evidence against this for two reasons. A) even if light cannot escape a black hole, it is still emitted from the atoms within it. In fact matter must sublime into light at a much faster rate under such incredible pressures as are found within a black hole and... B) ... I do believe Stephen Hawking recently came up with a theory that has been born out by other physicists (sorry I don't have a source atm) that black holes leak matter at their poles.
Light is massless and you are wrong about matter not losing its substance when it gives off light. Where there's smoke there's fire. The light is matter so to get light you must give up matter or to put it more precisely you must CONVERT matter and unwind it into light. All atoms everywhere are becoming less massive at all times. It may take an exceedingly long time for even a single atom to dissolve completely from thermal radiation alone - perhaps many trillions years - but it appears inevitable and inescapable that eventually all matter will have sublimed into light. ALSO f you dark matter , temperature without radiation is just silly . You're still an unproven hypothesis that may end up being nothing more than a skewed theory of gravitation - how can you have temperature without radiation?
Replace "light" with electromagnetic waves and yes. Although the one thing that stands outside this is Dark matter because it has no electromagnetic signature but it most likely has it's own version of decay also. The story that pops into my mind that reminds me that they know this to be true is the standard for 1 kg. They measured it a few years ago and found that it is getting lighter. Granted it will take hundreds of centuries before we would see a notable change but we can weight it so precisely that we can tell it's lost some between the last time and now. But yes, given enough time we know that the universe will spread out and all things will dissipate and decay into nothing. And by nothing we mean the universe will balance out to a particular energy level although to us it might as well be nothing. It's really just the second law of thermodynamics just over a much longer period of time. (I think it's the second law? The law of entropy)
If I understand your post correctly, what you're talking about correlates with the theory of Proton Decay. What you're specifically talking about I guess is post- Proton Decay, what will matter ultimately break down into.
The exception would be if the total amount of mass-energy that exists is sufficient to eventually halt the spacetime expansion and produce a "Big Crunch". Then you can kiss entropy good bye - for a while
not gonna happen. We know that the expansion of spacetime is a weak force that is easy overcome by gravity. So if two bodies are close enough to feel the gravity from one another then it will eventually come together but for the majority of the universe it's spreading out. Big Freeze is a closer description of what we currently think will happen.