Eons ago back when there was no record of time, no knowledge of the power that pokemon would soon hold over mankind. During this unknown time there were the ancient elementals, immensely powerful pokemon who had the power over the continents, the seas and the skies. The giant red ground type who would later be known as Groudon, with its claws it would carve out gorges and with the slam of its tail it could raise mountains, along with this power Groudon was able to conjure up a drought that followed it anywhere it wondered. It is said that he was destined to expand the land over the seas and conquer all of it as its own domain. The prowess that this pokemon had over the earth has never been matched.
But these actions gained the attention of the other elementals especially the blue whale-like behemoth Kyogre, who had absolute power over the seas; this power is second to none when it comes to water types. With the ability to stir up sweeping currents and tsunamis, much like Groudon, Kyogre has the ability to summon torrential downpours wherever he may be. He was determined to flood the lands and create a paradise for all water types. The final elemental was the serpent like Rayquaza, this green flying dragon claimed the skies as his own; it was his occupation to watch over the world but to never interfere with happenings of the lesser creatures of the ground. Legend has it that this pokemon could fly for extremely long periods of time, only coming down to rest and eat. He was naturally the most peaceful pokemon usually staying away from the fights that would rage down below as generally they never interfered with his skies. The only time that Rayquaza would descend was if fighting grew out of control and they escalated to the point in which they would be dangerous the pokemon and the earth.
As Groudon and Kyogre started to shape the world their elemental mastery, the fighting was few and far between, so Rayquaza never had cause to reveal himself to the world. The lands soon became lush with life, from trees and other plants to the very earliest, the seas were the same, slowly showing signs of life until both the lands and the seas were both teeming with life. These times were peaceful as they could be given that predator ate prey on a daily basis, but life went on it had to. Groudon and Kyogre still fought from time to time but it was only ever about small areas of territory and they generally ended quickly with one side realising that the risk just wasn't worth the reward. The millennia began to pass and the lands and the seas ever changed constantly enveloping each other countless times over the years.
But with time the fighting had become more and more frequent as well as ferocious, because of the fighting innumerable lives had been lost during these terrible times as both Groudon and Kyogre had become more vicious with their attacks meaning that they took less notice of the collateral damage that was occurring. Because of this the fighting had gained the attention of Rayquaza, although he did not yet believe it was time to intervene but to simply watch the fighting as it played out.
Groudon having been antagonised by Kyogre's floods over his land for the last time, he decided he needed to end Kyogre's attempts at ridding the earth of land once and for all. Meditating for years Groudon used all the strength that he had gained during that time to raise the earth around the pure white stone fortress that he had crated for himself, in doing so he released all the strength he had gathered in one fell swoop. The tiring Groudon looked out from the peak of his fortress, observing how effective his offensive manoeuvre had been, for as far as he could see monumental volcanoes burst through the earth's crust spewing red hot molten lava into the sea boiling it instantly, the lava that hit the land splashed everywhere burning anything and everything in its path. Unfortunately these volcanoes also sent giant plumes of toxic volcanic ash into the atmosphere almost blocking out the sun entirely. This action enraged the serpent like Rayquaza as it poisoned his sky. As Kyogre watched in horror from beneath the waves as Groudon reaped destruction upon his seas, he knew that something needed to be done and fast, so without giving any care to the damage that could be caused, he retaliated with a force so massive that the likes of which would not be seen again for hundreds of thousand of years. He brought down a wave so monumental it dwarfed the volcanoes in both scope and violence that it easily swallowed up the centre of Groudon's newly land, engulfing many of the fiery volcanoes.
After the seas had begun to die down from Kyogre devastating blow, did Rayquaza believe that an end must be put to the fighting that came with Groudon and Kyogre's reign of terror. Letting out a mighty roar that shook all pokemon but the two warring elementals to their very core, which sent every pokemon fleeing for their very lives, some of which hid deep underground locking themselves away from what would come next. Rayquaza dropped in from what seemed like the heavens as when he did the storms and the ash clouds dispersed as if he was calming and purifying the air that was near him, letting beams of light escape through the darkened skies almost as if a heavenly body was breaking through. The red and blue giants were visibly stunned at the sudden appearance of the green serpent, both creatures made it extremely apparent that they did not expect it, with Groudon stumbling over a newly formed boulder at his feet that he was going to use to fling at Kyogre as a weapon, and Kyogre crashing into a water fall that he had erected near an emerging cave to be used as cover against the others attacks. Rayquaza headed straight for the both of them, cracking his tail like a whip to disperse the storms and ash clouds, using his power over the wind he lifted the fighting giants into the air alleviating them of the fierce tempers that they were harbouring and sending them into a trance like state, after doing this he connected with the two pokemons inner essence taking it and sealing it away in a blue orb for Groudon and a red orb for Kyogre. With their essence gone the two pokemon were easily lead as they were ordered to bury themselves deep underground and settle into a deep slumber from which it would be impossible for them to wake from without the orbs being returned to its rightful host. With the loss of their essence Groudon and Kyogre were effectively turned to statues unmoving during their sleep.
Knowing that his role as the peace keeper and watcher from the skies was no longer needed as the fighting had been brought to an end, Rayquaza returned to the skies cradling the orbs he needed somewhere for them to be kept, sweeping the skies for a suitable location he decided upon a misty peaked tower that stood out amongst the flat land that surrounded it. Confident that the orbs would never be returned to the sleeping giants he placed them atop a pedestal at the peak of the misty mountain, flying down the side of mountain he noticed that this rock was fresh almost like at was created during the earlier fighting he also saw that the base of the mountain was flooded recently. Rayquaza realised that this structure must have had taken the combined efforts of both Groudon and Kyogre to create, they may not have known it at the time but they had created their own monument to themselves, it was almost fitting that the two orbs sat atop the mountain that both the pokemon helped create. Leaving the resting place behind violent thoughts began to encroach Rayquaza's usually calm mind, he thought about what would happen if the orbs were reunited with their hosts and the chaos that would be be released upon the world. These thoughts were pushed out of his mind as he knew it was impossible to reach the orbs as they sat atop a mountain whose face was vertical and therefore impossible to climb.
With the orbs out of reach and the pokemon slumbering, Rayquaza looked over the aftermath of the most devastating fight that he ever bore witness to, to the west the land had survived pretty much unscathed bar the single volcano that continued to spray a much lessened amount of ash on to the ground at its foot, but this was acceptable as this small amount of ash would allow for the ground to become fertile which would be the start of a budding habitat for many pokemon, the only other noticeable mark left by Groudon was the sand storm that had been whipped up in the desert at the centre of the landmass. Looking out to the east he was saddened by the vast amount of destruction that Kyogre's wave had left behind. The wave must have been larger than he first saw as the land had been almost completely sunk, bar an island far to east that had been split from what now was the mainland which had caves both to the north and south of it, one of which had a waterfall leading to it. Along with the island and it's caves Groudon's former white stone fortress had survived but now it sat at the centre of the new sea. Some smaller islands had also managed to survive the floods but none of which stood out, he knew that these were raised during the fight but none of them stood as high as they once did.
Happy that his work was done Rayquaza headed due south towards the pillar that reached high into the clouds, while he did know why it was here or what function this pillar once had, he did know that it was his adopted home that he generally used when he needed to rest from long haul flights or in this case stopping the potential destruction of the earth. He perched there knowing he had protected the world from a terrible fate, with that thought he drifted into a sleep, keeping his senses acutely aware of what was going on around him.
Had Rayquaza been able to understand the nature of time and history he would have known that in one way or another history had a funny way of repeating itself.