So, for example, time itself does not 'come into existence'. There is no time when time doesn't exist and a later time when it does.
Now, your assumption is that there was a time when matter and energy did not exist. That is almost certainly wrong. Even those physical theories that have the universe coming out of 'nothing' actually have a 'vacuum' state with energy. That energy is conserved in the development of the universe, but energy existed whenever time did.
A little incomplete, misleading, and needs clarification. Time did not necessarily always exist when energy existed, In the scientific view of the Quantum World, Quantum zero point energy is essentially timeless. In what we presently know of the the origins of our universe, the common hypothesis is time began with the expansion of the singularity and the formation of our universe as we know it. There is a relationship between time, energy and matter in this concept of the origins of our universe,