Pokemon's Canonical History 2/3 - Ancient History

All information is taken from in-game lore within the canonical games, therefore is the best understanding we have of the actual history of the Pokémon universe without speculation or fan-theory. Footnotes below.

See Part 1: The Origin Story Here

Around three hundred million years before the events of Pokémon, we have the appearance of the earliest known Pokémon, Genesect, who at the time was a common Bug Pokémon. Between two and one hundred million years before the events of Pokémon we have more known ancient Pokemon appearing, many of which are found in fossils. Kabuto, Kabutops, Omanite, Omistar and Aerodactyl being some of the oldest, likely dating to one hundred and fifty of million years old. Species then die out and new species appear and thus Pokémon change greatly over time. One hundred million years before the events of Pokémon lived the oldest known Pokémon species yet to go extinct, the Relicanth. Relicanth lived alongside the likes of Cradilly, Armaldo, Cranidos, Shieldon, Tyrantrum and Aurorus. Which have all been possible to revive through modern technology in the Pokémon world. Four hundred thousand years before the events of Pokémon lived Caracosta and Arceops. Each being the origins of their respective Pokemon types. Tirtuga and Caracosta the common ancestor to all turtle Pokémon, and Archen and Archeops to all bird Pokémon.

[1]&[2] One hundred thousand to twenty thousand years before the events of Pokémon, the humans appeared on the Pokémon world and migrated to every region. What Humans are and where they came from is still a mystery, though it is known that humans have always eaten Pokémon as food. [3]

Around twenty thousand years before the events of Pokémon an ice age struck the planet. The population of many Pokémon species waned, died out or changed drastically in these years, while ice Pokémon such as Mamoswine were abundant and thrived. The ice age ended around ten thousand years before the events of Pokémon and Mamoswine populations decreased. [4]

Three thousand years before the events of Pokémon a great war struck the Kalos region, it is unknown whether or not the war was between people and Pokémon, or just Pokémon, but Pokémon willingly fought in the war independently, and without Pokémon Trainers to guide them. One Pokémon who fought independently in the war was a Floette that belonged to a man named AZ, the oldest known Human. The Floette died in the battle, and AZ, wrought with grief, felt anger at the world for taking away his Pokémon. AZ, then built an ultimate weapon to end the war. The weapon took the lives of countless Pokémon and used that life energy to bring the deceased Floette back to life, and give it immortality. Due to being close to the weapon when this happened, AZ also gained eternal life. When the Floette found out many Pokémon died to return it to life, it left AZ behind. [5]

Two thousand years before the events of Pokémon, the Draconid tribes existed in a time when meteors fell from the skies near their home of what is now Meteor Falls. [6] The Draconid people were trainers of Dragon Pokémon, and their home was changed by the falling rocks. The meteors cracked the ground and created springs of primal energy from the earth, awakening the primal Pokémon Kyogre and Groundon after of sleeping for millions of years. The two ancient Pokémon battled over the primal energy and once again for dominance over nature causing massive destruction in their wake. The Draconid people prayed to the heavens and their call was answered.

Rayquaza descended and quelled the battling Pokémon. He sent Kyogre and Groundon to places where they may lie dormant once again. A rainbow stone now also existed, however, having fallen with the meteors, containing some of Rayquaza's power, and while the Red and Blue Orbs were held in the relative safety of Mt Pyre, the rainbow stone was held by the 'Lorekeeper' of he Draconid tribe. Rayquaza was then revered and worshipped by the people of the Draconid tribe.

One-Thousand Five Hundred years before the events of Pokémon, the first forms of the modern alphabet and written language was formed, baring a striking resemblance to the different forms of Unknown. [7]

One-thousand years before the events of Pokémon the primal Pokemon were just a passed down story to the Draconid people when a giant meteor fell and created the crater, now known as Sootopolis, but the subsequent destruction woke Groundon and Kyogre from their slumber, ready to fight yet again. With this, the Lorekeeper of the Drconid people used the Rainbow stone to make a wish that Rayquaza would appear and stop the fighting as it did before. Rayquaza felt the pull of the rainbow stone, answered the call of the Draconid people and Mega-Evolved. Rayquaza once again calmed the ancient Pokémon. This is the first discovery of Mega-Evolution. To commemorate this event, the Draconid people built the Sky Pillar, which Rayquaza occasionally uses as a resting place. Also, over the next two hundred years was the most recent time the legendary Pokémon Yvettle, capable of taking life energy and Xerneas, capable of giving life energy, went to sleep for a thousand years.

Part 3: The Contemporary History

Footnotes.

1. It is thought that many legendary Pokémon pre-date Humans. Very little is known about them, though they likely had a creator other than Mew. Legendary Pokémon usually only exist as the only member of their species, with some being reborn multiple times over millenia, such as Xerneas and Yvettle. Legendaries with unknown origins contain but are not exclusive to The Legendary Birds, Ho-Oh and Lugia, Latios and Latias, Heatran, Zygarde and Cresselia.
2. Canonically, any events in the Pokémon games that cannot be normally accessed, or Pokémon that are not clearly referenced in the main game does not happen in canon. This means that some Legendary Pokémon are actually Mythical Pokémon that are only assumed to exist but may not. These include Celebii, Victini, Darkrai, Diancie, Hoopa, Volcanion, Keldeo, Shaymin, Manaphy, Jirachi and Deoxys. With only Deoxys being catchable in any main story.
3. There are some legends that suggest that Humans and Pokémon were the same thing, or indistinguishable. There are other references that suggest Humans and Pokémon lives completely separately from each other – potentially due to being in seperate dimensions, which explains real world references in the Pokémon universe. Thirdly, the Pokémon Yamask is a ghost Pokémon who is said to be a human who has passed on, which ties humans and Pokémon eerie close together. However, all of this is speculation or non-canon, so humans remain a mystery in actual lore.
4. Between ten and three thousand years, civilisations rise and fall. Though humans and Pokémon were very close and people kept Pokémon – those Pokémon for the most part were still independent. Pokémon and Humans lived alongside each other. Most currently alive Pokémon species will have been around in these times, and humans remain relatively primitive in many ways of life due to the aid given to them by Pokémon.
5. AZ becomes an important traveller who appears in significant places throughout history.
6. Potentially a reference to the Litlenoid meteor shower?
7. It is uncertain whether Unknowns formed the shapes of written language or the language is based on the shapes of Unknown. It appears, however, that Unknowns can also exist in another dimension from the Pokémon world which is what makes them so rare. Unknown are capable of ancient powers; it is said that groups of Unknown begin to emit stronger powers the more of them there are.