However, due to the Law of Conservation of Energy, I suspect that energy will be all that is left, only in equilibrium meaning no ability for energy to form matter.
The law of conservation of energy states that energy is conserved in a closed system. This means the Universe, which is likely an open system, does not necessarily have to obey that conservation law. Not to mention, scientific laws are not absolute, despite their names; they are entirely empirical, and only apply as far as we've observed. As Edwin Hubble put it, "Beyond the limit of the observations, the form of [a] function, or relation, is speculative. For this reason, [a] law is empirical and it must remain empirical until it is explained by an accepted theory."
Anyway, let's get on with the answer. You've just described the Black Hole Era in the heat death scenario. If Hawking radiation occurs, then the black hole will continue to emit particles. During the last stages of its evaporation, a black hole will emit not only massless particles, but also heavier particles, such as electrons, positrons, protons, and antiprotons.
Once all black holes have evaporated, the Universe will be nearly empty, sans some particles that will almost never interract. Eventually, even the protons and antiprotons emitted by the black holes will decay into photons and leptons. Thus begins the Dark Era, when the Universe will be dominated by dark matter, electrons and positrons.
Electrons and positrons will rarely come together and form positronium atoms (in which the electron and positron are electromagnetically bound). Positronium decays very within nanoseconds, since the two particles annihilate. Thus, over time, the energy levels in the Universe will become lower and lower.
What happens next is a matter of speculation. According to Carroll & Chen (2004), quantum tunnelling and quantum fluctuations could hypothetically create another Big Bang, approximately $10^{10^{10^{56}}}$ years from now.
Adams & Laughlin (1997) speculates that quantum effects will dominate once all macroscopic matter is gone. Essentially, the laws of "macro-physics" will break down, while quantum mechanical phenomena prevail. As a result, the smallest perturbations would make the biggest difference in this era, so there is no telling what may happen to space or time.
Furthermore, they speculate that if the Universe is a false vacuum, the vacuum may decay into a lower-energy state, creating a new "child universe":
It is also possible for the universe to spontaneously create “child
universes” through a quantum tunneling process roughly analogous to
that considered above (e.g., Sato et al., 1982; Hawking, 1987; Blau,
Guendelman, & Guth, 1987). In this situation, a bubble of false vacuum
energy nucleates in an otherwise empty space-time. If this bubble is
sufficiently large, it will grow exponentially and will eventually
become causally disconnected from the original space-time. In this
sense, the newly created bubble becomes a separate “child universe”.
So yes, something as small as quantum tunnelling will potentially have an enormous effect on the future of the Universe.
In the end, we really have no idea what will happen after enough time, so there's no definitive answer to your question in the long run.
