For every one billion particles of antimatter there were one billion and one particles of matter. And when the mutual annihilation was complete, one billionth remained - and that's our present universe.
One always starts work with the subject, no matter how tenuous it is, and one constructs an artificial structure by which one can trap the reality of the subject-matter that one has started from.
The question of the origin of the matter in the universe is no longer thought to be beyond the range of science - everything can be created from nothing. It is fair to say that the universe is the ultimate free lunch.