Origins
Everything natural is, etymologically, everything that was born. The word comes from Latin nātūrālis, from nātūra — 'birth, nature, essential character'. The root is the verb nāscī, 'to be born', from Proto-Indo-European *ǵenh₁- meaning 'to give birth'.
Latin nātūra was Cicero's deliberate translation of Greek physis, and both words carried the same meaning: not 'the outdoors' but 'the way things are born and grow'. To ask about the nature of something was to ask about its birth-character — what it was from the beginning.
The root nāscī is spectacularly productive. Nation comes from nātiō — people born together, sharing a birthplace. Native means born in a specific place. Innate means born within. Pregnant combines prae- ('before') and -gnāscī: before the birth. Nascent means being born right now. Renaissance is a rebirth.
Scientific Usage
The narrowing of natural to mean 'of the outdoors' or 'not artificial' happened gradually. In medieval usage, a natural child was one born out of wedlock — the word's oldest sense of 'by birth'. Natural philosophy — the study of nature — was the original name for what we now call science.
The modern marketing sense — 'natural ingredients', 'all natural' — would puzzle a Roman. Nātūrālis meant 'according to one's birth-character'. Poison ivy is natural. Earthquakes are natural. Nature makes no promises about safety.