This is not the official backstory of the universe and is instead my own take on it. Do not take this too seriously
This chapter is a summary of what happened (again, in my vision of it). Later chapters will explain the full events.
Prologue: Summary
It was a dark, barren planet. There were rocks, some dirt. That was kinda it. However, Arceus, the Pokemon of creation, saw it as the perfect canvas for his vision. He wanted to make a planet that could have more creatures. Creatures other than just him, which he would soon call Pokemon.
The first two creatures that he created were to help him terraform the planet to fit his vision. He summoned the Continent Pokemon Groudon, and the Sea Basin Pokemon Kyogre. Groudon created the land, while Kyogre created the oceans. However, these two soon went to war with each other. To split them apart, Arceus made a third Pokemon; the Sky High Pokemon Rayquaza. Using it's power, Rayquaza sealed the two away. Luckily, they had created enough land and sea to hold life. However, there was one thing missing. Arceus knew that if he wanted to hold life in the planet, he'd need to give them some sort of fuel.
And so, Arceus gave Rayquaza a special purpose. It was now Rayquaza's job to create an atmosphere, holding oxygen to help the creature's in the planet live. The planet was still missing many more things, though. It needed light, and heat, so things wouldn't freeze. But it couldn't get too hot, as Arceus didn't want the planet to burn. So he summoned Lunala and Solgaleo, the Pokemon of Night and Day.
Solgaleo created the Sun, a large star that would bring both light and heat to the planet. However, Lunala created the Moon, a large asteroid-like body that was about three tenths the size of the planet next to it. The Moon reflected the light of the Sun to the other side of the planet, still giving it heat, but not too much. The night's were mostly cold. Arceus gave the planet an orbit. The planet spun around the Sun, while also spinning itself. And the Moon would orbit around the planet.
Arceus finally decided to name the planet. He named it "Earth," after the ground on it. Once Rayquaza had finished creating the atmosphere, he flew off into space. Arceus needed creature's to guard what Groudon, Kyogre, and Rayquaza had created. Thus, he created Thundurus, Landorus, and Tornadus.
Before he finally started creating normal everyday creatures, Arceus made Dialga, Palkia, and Giratina. Dialga created time, while Palkia created space. Giratina created the antimatter, however his actions got him banished to the distortion world.
The first creature Arceus created was the Pokemon Mew, who had very unstable DNA that easily allowed for it to turn into other creatures that were more stable. With this, Arceus could simply relax, and even Mew will mutate, and different circumstances would cause them to evolve differently and populate the planet.
There will be more events to the story, however this is a simple summary of the first few important events. There are still nearly forty Legendaries I have to include, and I haven't even mentioned Mythical Pokemon yet.