It would only be until the later stages of the earth that Rayquaza would learn to keep his ego (mostly) in check. For now though, Rayquaza had the type of mentality of someone you'd expect to have after single handedly defeating two primal gods, being worshiped and feared by primitive humans, ruling over all Pokémon of the sky in a tower that boldly defied logic, and just generally looking down at everyone. That is to say, he believed he was the greatest of Arceus' creations and was rivaled only by the Creator himself.
Rayquaza flew in spirals around the floating cloud fortress that was his Sky Tower. The Sky Tower, while technically located above Sky Pillar in the Hoenn region, was actually the very center of the sky itself, and connected to all areas everywhere through means only Pokémon of the sky knew. Rayquaza made this tower to give sanctum to all sky Pokémon, and as such, it can be accessed from anywhere and be used to access anywhere. Rayquaza was currently flying around it because he felt a nagging suspicion that it was getting smaller. After the Noctowls, Dragonites and Swellows assured him otherwise, he reached a new conclusion.
"My kingdom isn't growing," said Rayquaza to one of the Noctowls, "that's the problem."
The Noctowl wasn't really sure how to respond to this. He considered snark but then recalled that even though Rayquaza promised he would not destroy his loyal followers, accidents happened.
"Is there any way in which I might help?" Asked the Noctowl. He figured this would be his best approach; it might get him in Rayquaza's favor.
"Of course not."
There went a slight weight of worry of Noctowl's part; he was afraid he might actually have had to do something.
"You are but a mere Noctowl," continued Rayquaza, "but I, I am the almighty Rayquaza! I am the ruler of the heavens! I am the most powerful of Arceus' creations! So why am I confined to this small tower? My empire should extend and grow with my own magnificence!"
To Noctowl this sounded like words before an invasion and/or war, which just so happened to be the very thing Rayquaza was created to stop.
"Er, you wouldn't so happen to be planning to take over the Earth would you?" Asked Noctowl. Because if you are, I gotta make my way to Zygarde and fast, he left out.
Rayquaza burst into laughter for a while, which, unfortunately, sounded too much like the crackling of lightning, which is usually what followed after and not very pleasant when you're in a tower made of clouds. After he was done, he lowered his head to meet Noctowl's.
"Noctowl, I thought you were supposed to be smart. I rule the sky. What more of Earth would I want to conquer? No, what I want is the heavens themselves!"
Rayquaza made for a gap through the ceiling of the tower to reveal the starry night sky.
"Look at it, Noctowl. Those beautiful stars, those mysterious moons, those powerful suns. Clearly this is what I was made to rule! What you see up there is the true heavens. And as Arceus' greatest creation, it is only fitting that I take what is rightfully mine!"
Noctowl stared at Rayquaza in disbelief, then in fear. Disbelief because Rayquaza didn't seem to know that the concept of up meant nothing in space and that he also didn't know that stars and suns are the same and that stars are more powerful. Fear because despite this, Rayquaza had full plans to take it over anyway. Noctowl wasn't really afraid of what this would do to the balance of the universe, he was fairly certain that Zygarde would take care of that somehow. He was afraid that after Rayquaza left, Sky Tower would leave with him, and then Noctowl would be homeless.
Before Noctowl could beg Rayquaza to reconsider, the lord of the skies had already rocketed upward and into the night sky. Noctowl just stared at the green dot growing smaller and smaller. Nothing happened for the first few minutes. Then Noctowl and the other residents of Sky Tower felt a feeling of claustrophobia, the thing sky Pokémon hated the absolute most. Investigating the walls showed them that the walls of Sky Tower were definitely closing in and rising higher than most of them could stand to be in.
Tensions were rising and Noctowl wasn't sure what he was going to do next. He could flee, but he really didn't like the idea of being the first to run out of a crisis. He could stay, but in a while, there wouldn't be much of a place left to stay in. Noctowl had the disadvantage of being one of the few Pokémon that actually lived in Sky Tower. He was born there, raised there, and disliked the thought of living on the surface in trees and whatnot. He wasn't entirely sure what trees even were, but they sounded awful to him. Branches, leaves, fires, kids using other Pokémon to cut down and headbutt them to oblivion? No thank you. He'd rather stick to clouds and eat the berries that the Murkrow would bring in and forget about.
He was still considering his options when the Altaria began yelling in their awful shrieking "everyone get out of the way!"
Noctowl flapped his wings and backed up from the area he was in. Looking up, he saw what the Altaria were warning about. Rayquaza was falling towards Sky Tower like a green meteor and showed no signs of being in control of his descent. In fact, he looked unconscious. But before Rayquaza could make contact with the tower, he was suddenly frozen in place by a pink energy field. Lowering himself next to Rayquaza petrified body was a very angry looking Palkia.
"Would someone here like to explain why this overzealous snake decided to fly around my territory, screaming "Rayquaza rules all?" Asked Palkia.
Of course, no one answered him.
Palkia decided to get his answers out of Rayquaza, who he woke up by strangling by the neck and shaking violently.
"Can you explain why you decided to spell your name on my stars with that pitiful attempt of a Draco Meteor?"
It was hard for Rayquaza to talk in an arrogant tone while being strangled, but it didn't stop him from trying.
"Because I am Rayquaza! The mightiest of Arceus' creations! The ruler of the heav-AAAHHH!"
That was as far as he got before Palkia tightened his grip.
"Rayquaza, do you know who I am? I am Palkia, the ruler of space itself. I am in control of every molecule in every spec, every planet in every solar system, every star, moon and black hole in the entirety of creation. So when I hear you flying about my domain, acting and screaming like you own the place, I get a bit offended."
Palkia dragged Rayquaza to the nearest wall of Sky Tower and shoved his head out, showing Rayquaza the midnight ocean and dark mountains in the distance.
"This is your kingdom, Rayquaza. Remember that next time you get high and mighty. If you ever pull a stunt like this again, I can assure you that I will not be as friendly. And I get the feeling that Zygarde and Arceus wouldn't mind me beating a bit of sense into you." Palkia turned to the rest of the spectating Pokémon and said, "and let that be a lesson to all of you as well. As lord of space, there's one thing I know very well: no matter how big you think you are, there's always something bigger."
Some suicidal Braviary decided to ask, "what about Arceus? Is there something bigger than Arceus?"
Instead of blasting the bird into the smallest bits possible, Palkia just looked up, as if afraid of being watched, before answering, "yes. But trust me, you don't want to meet it."
And with that, Palkia rose off in a flash of pink light and the other Pokémon flew off into other places. All of them except Rayquaza. Rayquaza just stared at the night sky for a few hours. Noctowl wasn't sure what was going on in his head, and wasn't sure if he wanted to know. The universe was a tricky thing, he decided. Better he just mind his own.
A/N: The first of what I hope to be many Pokémon folktales I want to write and share. I'm a lazy person though. And for those who may be wondering, Zygarde is in charge of the entire Earth's balance as far as I'm concerned. I know Zygarde is a pretty worthless Pokémon in-game, but lore wise, it's probably one of the strongest.