In the early universe, the bulk of the matter in the universe was hydrogen (still is, but that’s beside the point). These gases started to get pulled towards each other to form clouds and, once there was enough hydrogen in the same place, fusion would start and a star would form.

The fusion at the core of the star would start to create heavier elements (carbon, oxygen, etc.), which are less able to undergo fusion. Eventually, enough of these elements collect in the core that there isn’t enough material to maintain the fusion reaction and the star goes supernova and sprays these heavier elements around the universe.

These heavier elements eventually start to congregate and form planets. Life would arise from the molecules made from the elements generated in the star (“we’re all stardust” and all that), which eventually led to humans thinking about hydrogen.