On and on the psychic went over cities and forests and crags. He spotted grimer and meowth; rattatta and sandshrew. There was even an occasional diglet too. He passed magnemite and electabuzz meandering about a human structure that emanated electricity in both his physical and psychic sight. And beyond that the immortal past the mouth of a river, where slowpoke and psyduck lay.
It occurred to the psychic then that his path had gone as far over land as was reasonable: going any farther north – especially to take the time to visit The Tree - might waste more time than necessary. And it wasn't like that place was a short way northwest from here to begin with. No, thought Myuu, he'd have to try to make time to return there after. Thus did he turn farther east, his flight path taking him over a cape. The edge of which, he saw, held a building with a round tower overlooking the cliff. He didn't remember it last time he was here, but no matter.
Once more over the open ocean, Myuu chose this time to dive within. Life abounded below the surface of the water. He waved at the schools of goldeen and magikarp as they went by. Northeast, Myuu swam, descending towards the seabed as he did.
A few minutes in, a massive shape passed by him, the being's pupils dwarfing the psychic's stature. It had been centuries, Myuu realized, since he last saw the giant dragonite. The last (so far as he knew) extant mortal to be modified in such a way by an ancient civilization that once lived here, the dragonite had still continued to grow since then and was quite clearly doing well. By all measures he was healthy and well fed. The dragon noticed him and smiled. Myuu responded by raising the edges of his mouth and sending the same brief telepathic greeting, before going on his way.
Deeper, Myuu plunged, passing horsea and tentacool and staryu. Three species made way for five for ten for twenty and so on as he went lower. This, all this is what he is for, Myuu thought, as he traveled along the continental shelf. He watched as numerous arrays of species passed by him. Some Myuu had created or modified himself, while others mutated into new forms on their own. Few of them were of the various original species to populate the area, he remembered. Most species didn't last forever. This was the way of things - that only the fittest survived. As much as he didn't like it, he knew it was inevitable. He had learned that long ago.
To descend deeper into Kyogre's realm, beyond the continental shelf, is to steadily enter a zone of twilight and then one of darkness. It is to lose sight of the sun; to lose its warmth. This is a forbidding realm where food is rare, and every calorie counts. The mortal denizens at this depth, some four thousand Myuu lengths or more below the surface, in the open ocean, are few and far between, and most know nothing of the sun above. Yet if one were instead to reach these depths by following the downward slope of the ocean floor, one might instead encounter places of great heat and life. From fissures in the ground, geothermally heated water and minerally rich smoke jet upward. Multitudes congregate around such vents, depending on them like lightless suns. Even here none can see, though typically it matters not. Above one such vent, however, this would not be so. Among those feeding off the smoke are individuals of a species that is new. And if one were to Flash a light upon it, one would observe a small bubble rising above it. One might even have heard a giggle.
Myuu reached out with his mind to take hold of his bubble, and pushed downward. As he pushed, so did he and his containing bubble descend. Down they sunk until the sphere sat on the mouth of the fissure. The Psychic smiled as he felt the pressure of the blocked vent oppose his own. Soon, thought Myuu, as he waited. A minute later, he smirked and let go. The bubble exploded upwards, the immortal laughing all the while. Not a moment passed after Myuu came to a stop that he descended back to the vent again for another go. Again and again, he rode the vent, until his extrasensory awareness noted the approach of another powerful mind.
"I should ask what you are doing," came the mental greeting of the newcomer.
"Waiting for Kyogre to show up around here. I want to show it this new species I made! Isn't it so cool? I know Kyogre comes by here from time to time, so I thought I could play here for a while I wait. …I haven't seen it for a while though. Do you know where Kyogre is? Can you tell me Uxie? Pleeeaseee?"
"It is apparent that you do not remember" stated the other. "Kyogre and Groudon were locked away again."
"Again? What happened this time?"
"They encountered each other again. And as always that leads to catastrophe, you knowthis. They have, with some exceptions, long since fulfilled their purposes anyway. Their active presence is no longer necessary. It has been judged that they shall remain asleep until needed once more."
"…oh.. " started Myuu, before perking up. "Okay! I guess I'll wait until Kyogre is awake again to show my creation!"
"Myuu… I do not think that the species will still be around by then."
"What do you mean, not around?"
"It will be a long time before they reawaken. Eventually you'll create enough new, fitter, species that will hunt or out-compete it or the ecosystem will change such that extant species will do the same until this species dies out."
Myuu scowled. "Nuh-uh. I'll just stop creating anynew species that interact with this biome until they're back!"
"I don't believe you. I don't think you will."
"Yuh huh! I can be patient! Even if it takes ten million years!"
Myuu could almost feel a projected 'raised eyebrow' when Uxie flatly stated "if you say so."
The Ancestor responded to that by sticking out his tongue in the direction of the Master of Memories, who then promptly vanished.
'Who did that know-it-all think it was – saying I couldn't be patient?' Thought Myuu. He'd show him. Really! Even if it takes ten million years! It was then that he remembered the continued presence of radiating heat. At that, the psychic returned to his fun. Life, Myuu thought as his bubble erupted upwards, is wonderful.
He had been correct, in the end, about his capacity for patience. The Ancestor had held back – lessened himself – from bringing forth anything new in most all of the ocean (most of anywhere really, given the era) as he waited for Groudon and Kyogre to re-emerge. Centuries had gone by, then millennia, then ages. It had been arguably the greatest act of self-control he had ever made. Eventually, the waiting finally passed a thousand millennia. He had happily refuted Uxie's doubts over his capabilities.
But Uxie too was correct, however. With that victory, his willpower had begun to falter. His resistance had worn out not a century later. Play had grown boring. Too many ideas had developed over that time. They weren't showing up. Even with Azelf's occasional help (by that point the only one of the other kami to support this self-denial), he could no longer do it. And so it was that his pent up imagination exploded into one act of speciation after another. It was not long before Uxie's predictions came to pass, and, without noticing, Myuu had allowed that gift of a species to fall into extinction. By the time the psychic had become aware of this fact, he had found that he had forgotten the species' design. Kyogre, when next it briefly woke, never saw it.
Myuu had resolved then to create a sanctuary of sorts where those species he couldn't bear losing could live on for eternity. That project had taken many geological epochs of work and experimentation. He had tried caves and isolated lakes but those didn't last with time nor were they certain to keep outside predators from swimming in. Massive psychic shields required constant maintenance. His success at bringing his descendants onto land had added further complications. With Arcy and Uxie's help he learned to call upon the power of the Unown. Experimentation had abounded then, much to the reclusive and antisocial Giratina's chagrin. Failed prototype after failed prototype had been tried; Experiments included everything from enchanted caves to runaway time bubbles. Finally, based on a comment by Celebi, he had landed on a solution.
It was an enormous rock formation like an oversized tree, combining the physical and metaphysical perks of both. Great Unown spells brought it to something resembling life, with its own internal immune system and temperature control - and stabilized by binding its 'life-force' to his own. Just as he was immortal and unchanging with time, so too would it. It had been improved over the years: the enchantments had been made more efficient, Celebi provided a plant network, which drew nutrients from the shared life-force embedded The Tree in time, and the Regis had been provided as gifts much later on to protect it. The structure had been developed just in time to rescue a number of variants of anorith from a major mass extinction.
Major flaws existed to the implementation, of course. Binding one's life force in mutual symbiosis also had downsides. There were times over the ages when external threats had damaged The Tree and him with it, requiring transfusions of aura to heal them both (Once upon a time, it was Arcy who had done so for him. Arcy was gone now, and the transfusions typically fatal to the aura adepts who did so in the Original One's stead). But there had never been a scenario where the damage went the other way, the psychic remembered. Myuu didn't know what the outcome of the recent battle would have been had it not been interrupted. How fit was he really, compared to Myuutsuu? If something were to happen to him, how long would The Tree survive? He didn't want to think about it. The psychic sighed and moved on.
AN: 1) That's my interpretation of where the Tree of Beginning comes from and why it exists, as well as a look into the Pokémon worlds geological past. I put way too much research into this to make things chronologically fit with IRL deep time. The way I see it, like much else involving Mewtwo, Mt Quena is (unbeknown to the clone) a reflection of the Tree of Beginning in the place's role as a sanctuary for pokémon that have no place in the world.
2)I had waited to upload this for a few months because I intended to have a second half showing what happened to Samiya before Mew resurfaced, but I couldn't get it to work logistically.