Pokémon Creationism

Arceus was born from nothing, not even chaos.

Arceus soon made Dialga, Palkia, and then Giratina. Dialga created time, Palkia created space, and Giratina created anti-matter. And thus, the Universe was born.

Dialga, Palkia, and Giratina began battling and as a result were banished to their individual realms by Arceus.

Arceus then created Groudon, Kyogre, and Rayquaza. Groudon formed the huge celestial bodies known as planets, and the trio chose one to inhabit with life. Arceus created the sun, then shot off across the universe to create all the many stars.

But he had learnt from experience, so he tasked Rayquaza as the peace-keeper.

The trio set to work, with Groudon raising land violently, creating volcanoes and mountains; Kyogre, creating the seas, where the land was not, and Rayquaza making an atmosphere full of 'air'.

Sure enough, Kyogre's waters started to corrode Groudon's land, and this angered him. The two battled, but Rayquaza broke it up, and sent Groudon deep underground, while Kyogre was sent deep into the oceans, before returning out into the ozone layer.

Soon, Arceus returned, and it tried to make life, but failed miserably. So it created Regigigas. Regigigas moved the continents with its bare hands, piecing them together like a puzzle.

When the final chunk of land was put into place, the world sprung to life, with grass and trees sprouting everywhere. Finally, the world was ready for life.

Arceus sent Regigigas into a coma until it was needed once more. It then created thousands of Pokémon to inhabit the world. These Pokémon belonged to one of five races.

Celebi   Jirachi   Mew  

Manaphy   or Victini  

It also created Latios and Latias, its personal agents, whom it sent flying through the universe in search of a species with great intelligence to live in harmony with its creations, before leaving once more to regain energy.

      

After much searching, Latias found an intelligent alien species known as Deoxys. They were bacterial but advanced. They chose a few of them and brought them back to their world.
  
For a while, things were fine, and the Deoxys and natives lived together in harmony. Until the Deoxys discovered they could 'infect' the natives and use their bodies. Suddenly, they were all infecting a host, and then war broke out.

The Mew, Jirachi, Manaphy, Celebi, and Victini battled their infected brethren to set them free, while the Deoxys sought total dominance.

The war raged on for many centuries, until there were but a handful left of each species. Arceus returned and destroyed the last of the Deoxys, but the damage was done. The population of the world was little more than 20.

The Celebi retreated to the forests, hiding amongst the trees and in time. The Manaphy retreated to the sea, the Jirachi fell asleep, only waking up every so often, and the Victini hid in far-off lands.
This left only the Mew.

During the war, three Mew had hidden under lakes in search of enlightenment.
          
               
Leaving only a handful of Mew left to roam. They were alone.

The war had left the land in ruins; some places were battle-scarred beyond repair. Instead of lush grass, there were harsh deserts. This angered Groudon, sending him into a rage. Volcanoes spurted and spewed lava everywhere.

One day, a Mew was floating along when a sudden flow of lava approached it. Thinking quickly, Mew unleashed energy inside it that even Arceus didn't know about. It morphed the lava into a form and gave it LIFE. The first Heatran was created.
 

Arceus sensed this and had an idea. Gathering all the able Mew, it channeled immense power through them, using their life-giving abilities to create more living creatures. These were crude and unfinished, prototypes of what was to come.

Aerodactyl filled the sky, while Lileep, Cranidos, and Shieldon roamed the land.

Anorith, Omanyte, and Kabuto populated the seas.
  

Arceus also bestowed upon most of these beings the power to 'evolve' into more powerful creatures if the correct environment was met.

Finally, Latias returned once more. They had been far more thorough in their searching than before. However, Arceus had told them to stop, but guilt kept them going. They were determined to complete their job.

They brought humans from another planet. Basic but intelligent beings who definitely lacked the ability to infect anything. The humans settled in quickly, initially living relatively separately from the animals.

But Arceus wasn't convinced; he felt the need to test them.

First, Arceus created Articuno, who he ordered to send the planet into an Ice Age.
  

Articuno froze the planet, killing many creatures, but giving birth to new ones like Mamoswine.
  

To Arceus' pleasure, the humans adapted, creating structures out of ice and snow. The severe drop in temperature awoke Regigigas, who rose high above the land and saw what was happening.

The humans instantly fell in love with Regigigas, worshipping the titan and creating statues of it from ice. Touched by this, Regigigas found one of the statues and breathed life into it before returning to sleep.
  

However, this scared the humans, and they locked it away in a cave.

Realizing that the Ice Age did not affect the humans, Arceus created another bird, Moltres, and ordered it to send the world into a drought. The ice melted, and the water evaporated as the temperature rose higher and higher.
  

While the humans continued to adapt, using the skills they had learned with the ice and applying them to rock, the creatures weren't as lucky. The Mamoswine and other creatures that adapted to the cold died off, but new ones such as huge insects like Yanmega became common.
  

Once again, the drought awoke Regigigas, who once again saw a statue of himself. Thinking the humans would have learned from last time, Regigigas gave it life. But rumors of the living statue had been passed down and exaggerated since last time, and once again, the scared humans locked away this second 'Regi'.
  

When the drought finally wore off, Arceus began the third and final test. He created one more legendary bird, Zapdos. Zapdos created powerful electrical storms all across the land.
  

The storms killed off the last of the prototype creatures, leaving only the humans and the few pets they brought from their home land. One extremely intelligent man managed to harness the power of electricity, creating the first electronic device.

Of course, Regigigas awoke one final time. He discovered that the humans were far more evolved than expected, able to harness metals and electricity, albeit at a somewhat primitive level. More out of tradition than anything else, Regigigas created the third Regi out of steel. The humans were no longer scared of this Regi, but they sealed it away with the other two nonetheless, knowing that one day someone powerful enough would tame them.
  

Arceus was baffled. The humans had passed all three tests of harsh weather. Zapdos calmed the storms, and the world became peaceful once again.

Arceus herded the Mew together for a second time. Having learned the strengths and weaknesses of his prototype beings, Arceus was ready to go farther.

Siphoning its huge power through the small pink beings, Arceus filled the world with hundreds of species of creatures that would become known as 'Pokémon'. They were more diverse than it had ever imagined, filling the skies, land, and sea.

The life energies even reacted with the sun rays and moonlight, creating Ho-oh and Lugia respectively.
    

Some radiated out of the planet's moon, creating a population of Clefairy, as well as Cresselia on the light side and Darkrai on the dark side of the moon.
      

Lugia befriended the three elemental birds, and they followed him like a leader. Meanwhile, humans started to get closer to these new creatures, using them as slaves, weapons, or pets. The term 'Pokémon' arose from strange travelers and stuck.

The first Pokéballs were created from Apricorns, and the bond between human and Pokémon was complete.
    

Ho-oh took residence at the top of the Bell Tower. It was jealous of Lugia's trio of birds and wanted one of its own. One day, three Kimono girls entered its tower with a Jolteon, Flareon, and Vaporeon.
      

Ho-oh burnt down the tower with its Sacred Fire. Most escaped, but the three Pokémon were trapped and perished in the flames. Ho-oh soon resurrected them as Entei, Raikou, and Suicune.
      

Humans continued to evolve and take over the land, and Pokémon continued to work alongside and for them for many, many years.

That is the story of the Pokémon World.