Purges were periodic events during the Ancient History of the Pokémon World. They consisted of the systematic eradication of much of the Pokémon World's biodiversity by that point by a number of agents, most notably the Lake Trio a handful of times, taking place during the early Eras.

The context for most of the early Purges was a need by the Creation Trio and Lake Trio, by then still largely inexperienced with creating or managing life, to toss their current progress into the bucket and start anew with new or improved designs and different, usually stricter limitations in place for the abilities of the various creatures they spawned.

In order to proceed, the instigator of the Purge, usually a member of the Lake Trio, would spawn powerful agents who, granted an amount of divine power, would spread around the Pokémon World exterminating the various species living there as they went. Other times, the purge would take place by triggering large-scale disasters that would reshape the Pokémon world, events usually kickstarted by Dialga or Palkia. Finally, a few number of times several members of the Sextet would join forces and flat out change the fundamental rules of the universe around them, including thermodynamics or gravity, to the effect of instantly making several creatures suddenly unable to survive or even exist as entities in the world.

At least the former two methods left enough traces of the early species that they were able to build up into the fossil record. Kabuto and Anorith for example are fossil records originating from different Purges across the early Eras.

In the very few Eras the Lake Trio felt strongly about their creations and did not have the “heart” or the experience to go with a thorough purge; as things were, this allowed some species of Pokémon to survive into the next Eras in small numbers; most of them went into hiding for some time and only chose to surface later, once their old, more unique powers had acclimated to the rules of the new world, some of them eventually becoming part of what we today call Legendary Pokémon. A particular case are the last specimens of the species of Rayquaza, Kyogre and Groudon, who survived the latest batch of Purges and eventually built up enough power to become threats to the world even reaching to the The Present Era.

Over the more recent Eras there have also been Purge-like events where much of the Pokémon world landscape or biodiversity has been reshaped or remade, though not to a level as extensive as it was back then during the early Eras. Probably the most notable event of such kind was the Previous Era period of time known as “the Rain”, which lasted for over 400 years and forced many hiding Legendaries to resurface and assume the roles we know them by today, such as Lugia and Yveltal.

The release of the Kyogre and Groudon in 3733 PE was intended to be a new Purge, to start a new Era, but the world was spared this fate once Rayquaza achieved his own Primal Forme, allowing him to curbstomp the waging Legendaries.