The legends of the Cataclysm have endured surprisingly well from word of mouth. In it, the world was divided between six major nations that were engaged in an aggressive free-for-all war. The catalyst for this conflict was a one-of-a-kind artifact known today as the Remnant, a stone that contains the power of creation. Under its influence, several Pokemon either transmutated into more powerful beings or fully ascended into godhood. The desire to control the Remnant lead to escalating conflict that wreaked more and more havoc.
Then, without warning, the world was attacked by The Creator. Crashing down upon the world, it started annihilating everything it saw. Half of the nations were completely obliterated before the others realized the scale of disaster they faced, but even cooperation between these rival groups could not stop it. Details of how these last three nations fell are scarce, but artifacts of data indicate that the combined forces of all three nations came together, presumably to face The Creator. Obviously, they were defeated.
How the Cataclysm was stopped remains a mystery. With most life eliminated, The Creator formed several destructive Amalgamations of spirits out of elemental gems forged from his essence. With a monster for each Pokemon type, these Amalgamations were designed specifically to hunt down every remaining semblance of life. However, shortly after the creation of these monsters, they were all destroyed and their gems went missing. The Creator itself presumably was stopped shortly after, but no record exists of how it was defeated.
What little life remained had been forced underground due to how uninhabitable the surface had become. It took several thousand years for the world to grow to a habitable state again, whereupon Pokemon life finally returned to the surface. Life continued to exist in isolated pockets for several thousand more years. Only in the past ten thousand years have Pokemon dared to begin exploring the world.