Thousands of years ago, the Hoenn region was a peaceful place. Pokémon and humans lived together in harmony, and balance made the world as tranquil as it was. Surely the people were blessed by the calm, and chaos was rarely a word in their vocabularies.
Nestled deep within a cavern on the western side of the region lived a civilization of Dragon-type users, known simply as the Draconids. They lived alongside their Pokémon, taking care of their village and each other and rarely venturing outside. There was no need to - they had rich soil in which to grow food, pure water from the waterfall flowing within the cave, and many ways to entertain themselves. Mural painting, storytelling, and Pokémon battling kept their days interesting. However, since they were cut off from the rest of the region, they had no foresight of the impending doom that was soon to come.
In the eastern part of the region was a second cavern. This one housed people as well, known as Sootopolitans, but it also housed the Legendary Pokémon, Groudon and Kyogre. The Sootopolitans lived in a constant state of fear, as the energy they had cultivated from the cave for so long was being fought over by the two greedy titans. In order to appease these two powerful creatures and quell their incessant fighting, they would sacrifice bits of the energy they had gathered, as well as food and cloth. After some time, they realized the two Pokémon were only after the energy, which they dubbed Infinity Energy as they learned of its power.
The leader of the Sootopolitans diverted a large amount of this energy into three orbs - one of ruby, one of sapphire, and one of emerald, placing two of them at the feet of the two Legendary creatures so that they would stop coming to the denizens in search of energy. The third orb, the emerald orb, was kept sealed within a chamber of the cavern, only to be used if the fighting between Groudon and Kyogre got too out of hand and the other two orbs were rendered useless.
The Sootopolitans' strategy was a failure. The energy contained within the two orbs, simply called the Red Orb and the Blue Orb, was too much for the two Pokémon to handle at once, and they transformed into hideous creatures. Light flowed through their veins, and they reverted back to the primal forms the people had only heard of in myths. Soon, the two Pokémon burst forth from the cave and rampaged, bringing destruction across the region. The Sootopolitans were horrified at the chaos they had wrought, but they continued to lay low in the hopes that no one would trace the carnage to them.
The sky was torn asunder by rain, then sun, then rain again. The rapidly changing weather killed the crops, and the harsh sunlight and torrential rains tore the land apart. The people of the region begged for something to be done about the destructive force of the two Pokémon, but none of their partner Pokémon were strong enough to defeat these primal entities.
One day, however, peace rained down from the heavens in the form of a meteor shower. The meteors struck the cave of the Draconids, and while many were able to flee, many more perished in the downpour of rock and fire. As the meteoroids struck the waterfall, they glowed with an ethereal rainbow light, and in the sunshower above them, the clouds parted. Floating above the clouds was a serpentine creature, an emerald green dragon with a black and yellow pattern snaking down its body. It descended and greeted the people of the cavern at which the meteroids struck, mesmerized by the rainbow light emanating from them. The Legendary Pokémon, who was henceforth known as Rayquaza, then took to the skies and rushed to the middle of the Hoenn region, where Groudon and Kyogre had taken their quarrel.
As Rayquaza roared, the screech reverberated throughout the entire region. Groudon and Kyogre, swayed by their master's plea to cease their fighting, backed down, and they retreated to separate caves so that they could work off the rest of the excess energy in peace and quiet, without having each other to argue with. Rayquaza's powers turned the weather back to normal, and the region was reverted back to its original tranquility. As Rayquaza returned to the skies, the Draconid people regarded this Legendary Pokémon as not only a hero, but a deity. They worshiped Rayquaza as if it was a god, hailing the Pokémon as sacred in the waterfall village, which they named Meteor Falls.
However, peace did not reign supreme forever. Once again, a thousand years later, the meteoroids fell. This time, they struck the Sootopolitans' home, the cave they dubbed the Cave of Origin. Like what happened with the Draconids a millennium prior, many of these people died in the ruination of the cave, but many more survived to tell the tale. The surviving Sootopolitans feared that the damage caused was because of what their ancestors had done one thousand years ago, and in order to atone their home had to be destroyed, but the crater caused by the meteoroids paved the way for a new home to be made. They named this new place after themselves - Sootopolis.
But the meteoroids did not just create Sootopolis. They also upset the natural balance of energy in the region, and the upswell woke Groudon and Kyogre from their deep slumber, a slumber that had been caused by them running completely out of the energy they had taken from the two orbs created by the Sootopolitans. The two Pokémon emerged once more from their separate caves, once again having reverted to their primal forms thanks to the copious amounts of energy. The people went into a panic as they ran amok once again, bringing destruction wherever they went. The disasters they brought only became more threatening to the wellbeing of the people, and they prayed that Rayquaza would restore the balance as it had before.
The meteor that had caused the crater that created Sootopolis glowed with the same rainbow light as the meteoroids that had landed at Meteor Falls, sending a beacon to the heavens. The sky parted once more, and Rayquaza descended, hearing the Hoennian people's desperate plea. Though this time, it did not fly to Meteor Falls. No, this time it went to the new city of Sootopolis, where a bigger, brighter, more luminous and beautiful meteor was held. Rayquaza swallowed the meteor whole, and as it did it glowed with the same ethereal rainbow light as the meteor. This was no regular primal form - this was Mega Evolution, and the very first instance of it in the world. Now more powerful than anything the people of the region could comprehend, Rayquaza traveled to quell the rampaging Pokémon.
Vicious winds whipped through the region. These winds calmed the storms and dimmed the sun, calming the fighting Legendary Pokémon almost as easily as last time. After they calmed down, Rayquaza and the Sootopolitan people sealed Groudon and Kyogre within the people's old home, the Cave of Origin, where they were guarded closely by those deemed strong enough to keep them in check. The Red and Blue Orbs were transported to Mount Pyre to be looked after as well, and as Rayquaza returned to the heavens once more, it was up to the Sootopolitans to decide what to do with the green orb, which they named the Jade Orb.
With the help of the Draconids, the Sootopolitans built the Sky Pillar in the southeast area of the region, amidst the whipping waves of the ocean. This pillar was created to be a home to the Legendary dragon, and a temple where the Draconids and Sootopolitans alike could come and pray to their savior deity. The Jade Orb was also placed at the top, filled with the energy needed for Rayquaza to Mega Evolve once again if it was ever needed again. The two peoples used the Sky Pillar to bring themselves closer to Rayquaza's domain, and to each other as they worshiped the same deity.
Soon, the Draconids became paranoid that the meteoroids would strike again, upsetting the two Legendary Pokémon once more. They eventually devised a plan that would prevent this from happening again, but they realized that the only way to fully prevent it was to betray the Sootopolitans and prevent them from entering the Sky Pillar. With heavy hearts, the Draconids sealed the Sky Pillar and guarded it heavily, allowing only their own people to access it. Infuriated and angered by the betrayal, the Sootopolitans attacked and raided the Sky Pillar, taking the Jade Orb back and leaving the monument defenseless. They destroyed the Jade Orb - their own creation from ancient times - out of spite and sadness.
The two civilizations did not speak to each other at all after that. They developed their societies separately, refusing to fight as Groudon and Kyogre had out of indifferent respect for each other and hesitation to make war like the Legendaries Rayquaza had stopped in fear of it bringing the same wrath upon them. Instead, a Cold War began, though over time generation after generation forgot about the silent rage the two civilizations felt against each other. Each one forgot the other existed and lived in blissful, ignorant harmony, awaiting the next meteoroid strike.
…
As he reached the top of the Sky Pillar, the black-haired woman was waiting at the top. Her raggedy cape fluttered in the evening breeze, and she was cradling her Whismur in her arms. As she sensed his presence, she turned and smiled. "I see you enjoyed my tale," she said. "Now you understand why I must do this, yes?"
He nodded. "I understand, Zinnia."
"Thank you, Brendan. Thank you for helping me save my people. I will never forget what happened this day." The lorekeeper turned around once more, facing the Dragonhark Altar as she raised her hands in the air. "Now, Rayquaza, hear my fervent wish! I summon thee, for my people - the Draconids!"