Except probably hydrogen :v
Also, microwave background radiation is the residual heat/radiation from the big bang... I guess eventually it'll settle down to near absolute zero (it's within a few degrees right now)
You can't destroy energy, but it can and will spread out thinner and thinner, until eventually every little photon is flying off in some trajectory that has a 0% chance of ever intercepting a black hole.
As has been said before, black holes evaporate (larger evaporate much more slowly though; so their evaporation comes more in the form of sparks of radiation as the wink out of existence, with nary a trickle until then). In about 10^14 years, star formation stops (and with it, the formation of any considerably sized black holes). In around 10^100, black holes are expected to all evaporate. So that's the boring stuff of our current universe.
Depending on the end result of macro-scale physics, weird things may happen after this.
There's the "Big Rip" idea, in which expansion accelerates and makes macro-scale physics meaningless; though I've not actually heard much support for this. Big Crunch theories were fairly standard originally; of course, then we discovered the expansion was accelerating. So there's that general category of 'ends' to time.
Then there's the alternative, in which over strange eons, even the death of the universe may die.
https://en.wikipedia.org/wiki/Poincar%C3%A9_recurrence_theoremEssentially, infinite time overrides chaos and entropy. These are both based on statistical rules; and when you introduce infinities to statistics, you end up with a result in which all possibilities eventually happen, albeit with unimaginably vast eras of boredom in between. Even the evaporation of black holes is beyond the time scales we can possibly fathom; but is only a tiny blip in time compared to these. After all, it is literally the amount of time it takes for random photons and fluctuations at the quantum level to spontaneously start off a low-entropy event similar to the big bang. Ridiculously vast, beyond comprehension or imagination. Beyond Lovecraftian. So yeah. Over infinite eons, statistics dictates that even the death of the universe will die (assuming no event first occurs to rip apart time itself).
That, of course, is speculating based on known physics. So far as we know, it may well be turtles all the way down, and there may well be a larger, timeless multiverse (linear time being a property of this universe, and tied up with its space, we don't really have a reason to think it would exist/be the same outside of the universe).