primordial, undifferentiated substance from which everything begins
So, the Cosmic or Primordial Soup?
Primordial soup, also known as, primordial goo, primordial ooze, prebiotic soup and prebiotic broth, is the hypothetical set of conditions present on the Earth around 3.7 to 4.0 billion years ago. It is an aspect of the heterotrophic theory (also known as the Oparin–Haldane hypothesis) concerning the origin of life, first proposed by Alexander Oparin in 1924, and J. B. S. Haldane in 1929.
As formulated by Oparin, in the primitive Earth's surface layers, carbon, hydrogen, water vapour, and ammonia reacted to form the first organic compounds. The concept of a primordial soup gained credence in 1953 when the "Miller–Urey experiment" used a highly reduced mixture of gases—methane, ammonia and hydrogen—to form basic organic monomers, such as amino acids.
You can think of this metaphor as a myth of sorts, especially since before it was a "scientific hypothesis" it existed as the primordia materia in gnostic and alchemical works. But you might be looking for something a bit more ancient.
But you're probably looking for something more ancient.
I think one obvious example is the "deep" in Biblical and other Near Eastern mythologies. This is represented as water, and probably really literally meant the ocean before land. You have to imagine how unimaginably mysterious the ocean must have been before modern video equipment documented it, especially since it still is rather mysterious.
So in Genesis (1.2-5), the "primordial soup" is the "waters" upon which Yahweh hovers:
The earth was without form and void, and darkness was over the face of the deep. And the Spirit of God was hovering over the face of the waters. And God said, “Let there be light,” and there was light. And God saw that the light was good. And God separated the light from the darkness. God called the light Day, and the darkness he called Night. And there was evening and there was morning, the first day.
Similar myths concerning land from water are found in Tungusic and Finnish myths.
Chinese myths also have this origin in the story of Pangu. From Wikipedia:
In the beginning, there was nothing and the universe was in a featureless, formless primordial state. This primordial state coalesced into a cosmic egg for about 18,000 years. Within it, the perfectly opposed principles of yin and yang became balanced and Pangu emerged (or woke up) from the egg. Pangu inside the cosmic egg symbolizes Taiji.