The question is reasonable, I just don't know where you got the idea of ''one hydrogen atom'' from. It's not an idea that comes from science.
As for the ultimate origin of the singularity: nobody knows. There are plenty of things that are poorly understood or not known.
There are ideas put forward by science, colliding branes, various multiverse models, oscillating universe, etc....theories based on our current understanding of astrophysics...being a work in progress.
Contrary to science, religion has all the answers, and they all are or were very certain of the truth: Yahweh created the heavens and the Earth, Brahma is the one, Allah is the one true God and Creator, Enki, Ahura Mazda, etc, etc....the gods of the gaps.
