Nobody knows how the universe began but by observing the universe today and by using telescopes that effectively allow us to look back in time the most widely accepted theory is the Big Bang theory.
This theory suggests that at one time all matter was compressed into a single point, not two points or anything else, everything was contained in one single point that exploded into the universe.
Could that happen again? Well there is a theory called the Big Crunch that suggests that at sometime in the future the universe will stop expanding and begin to contract and that it will continue to contract until all matter is a singularity again, this singularity could explode again into a completely new universe.
There are many other theories about universes, both ours and many, perhaps infinite others sometimes existing in parellel dimensions to ours but none that I know of that suggest that our universe will be wiped out by two ordinary particles colliding.