Onix are a pokemon of great antiquity, which dominated the land in the Paleozoic age. The grass types which existed at the time could beat Onix in combat, but they had no reason to do so: they were largely stationary pokemon ancestral to creatures like Oddish and Bellsprout which preferred to leech from equally stationary rocks. It was in the Triassic, with the rise of saurian pokemon such as Sceptile, Meganium, and Venusaur, that the Onix went into decline. These fierce pokemon were capable of leeching their nutrients and wrapping them with vines to prevent escape, moved at far greater speeds than them, and often exploited Onix's weakness to so-called "special" attacks such as Solarbeam. Hunting by these pokemon drove the Onix from most of the earth's surface, and they turned to seek shelter in the caves where they are found today.
(Indeed, given that the pokemon are made of rock, it is occasionally even the same Onix. Onix do not live forever, but their bodies do: it is the mind which decays and shuts down until another mind forms. Their great age allows them to be considered "living fossils" in more way than one.)
A recent development, however, threatens to change the balance of the ecosystem. Some Onix have fashioned discarded steel from human settlements into coats of armor which fuses into their very cores. These steel Onix or "Steelix" are considered to be a new evolution of Onix, and (despite their numerous weaknesses) are immune to the electric pokemon which are most often the natural predators of steel. Colonies of this pokemon have thus far only appeared in Sinnoh and Johto caves, but there is ample reason to believe that, as their population grows, they will crawl across the outside ground once again.
I would like to thank EvilFuzzy9 for giving me the idea for this entry, and to belatedly thank snochaoko, Lyraeon, and Vethica for helping me with earlier ones.