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Papery, adjust your siggy so it doesn't stretch the screen from here to Timbuktu!

In the beginning, there was only The One. Arceus, Ruler of Eternity, The God of all Pokemon. Arceus lived alone in the universe- then the size of a grain of sand. But It was driven to create. Then from it emerged three beings:

Dialga, Pokemon of Time
Palkia, Pokemon of Space
and Giratina, Pokemon of Matter.

Giratina defected from Arceus, and quickly vanished to another dimension, and the other two set about creating the galaxies as we know them. But the Master was unsatisfied with the emptiness of the universe, so he then created another egg, which contained:

Uxie, The Being of Knowledge,
Mesprit, The Being of Emotion,
and Azelf, The Being of Willpower.

The Pokemon of Thoughts. The egg stayed dormant, while another egg emerged from the Master:
Cresselia. It and Dialga and Palkia now created the stars in the sky, and the many planets and moons. The most prominent one would be inhabited by all of the trainers: The Pokemon World.

Meanwhile, yet more Pokemon were separated from the form of The One:

Rayquaza, Ruler of the Skies
Kyogre, King of the Seas
and Groudon, Titan of Earth.

These three, however, broke away from the Emotions and began to wreak havoc on a certain world, defining it from all other worlds.

In the horrendous clash, continents were shaped, clouds formed, and seas
stormed. Eventually the Master was forced to make a pokemon that did not fit the mould:

Deoxys, The Being of Instinct

Deoxys was the first pokemon created by the master in multitude. They descended to the newly formed planet and the pokemon titans were forced to unite and drive the Deoxys back away, deep into the recesses of space...

The Original Feud had been settled, but the Pokemon World was now defined by
many definitive areas:

The Kanto Region, a moderately flat country.
The Johto Region, Sister to Kanto.
The Orange Islands, fraught with mystery.
The Hoenn Region, a largely oceanic place.
The Sevii Islands, secluded far, far below Kanto.
The Orre Region, strewn with deserts and dangerous sandstorms.
The Fiore Region, a lush landscape with many secrets that later became a
refuge for legendary Pokemon.
and The Sinnoh (Shin'tou) (Sintoh) region, home of the most pure lakes, divided by
mountain ranges.

Now, the Beings of Thought came out of their shells. They appealed to the Master, seeking to do his bidding. The Master looked on to the Universe, and noticed that for all the scenery, the only live forms were his servants. So he bid them (all the "Legendary" pokemon created so far) think for themselves and become independent.

The Beings of Thought combined their powers and created the first humans. But soon, from the darkness on the fringes of creation, there came a new pokemon which The Original One had not created: Darkrai, The Darkest Soul. Darkrai came to the humans in secret, disguised as one of them, and tainted their thoughts with dark whispers of their right to rule over all pokemon, even Arceus himself! But when Cresselia's revealing light showed Darkrai for who he really was, the humans beseached Arceus to forgive them and help them banish Darkrai. Darkrai became enraged, and he took to a duel with Cresselia. The battle was long and difficult, before finally, Darkai struck Cresselia down. Just as all seemed lost, though,there came from another dimension the Unown, The Causality Distorters. They surrounded Darkrai, whose power had been spent in the duel, and imprisoned him upon a desolate island. They then said that so long as no human set foot within the sanctum that held Darkrai, he would remain there forever.

The Master noticed the amount of difficulty Darkrai's defeat had taken and decided more multiple pokemon, like the Deoxys, would be created for the human's friendship and defense. Some of the earliest pokemon (in no order):

Aerodactyl
Shieldon
Bastiodon
Kabuto
Kabutops
A Prehistoric, much more powerful version of Magicarp.
Gyrados, at this time the most ferocious pokemon.
Omanyte
Omastar
Lileep
Cradily
Anorith
Armaldo
Eevee
and possibly some others. Many of these pokemon became extinct and were buried
as fossils in remote places like the Desert Area and the Sinnoh Underground.

Then the Master created minor guardians of different areas, with instructions to the humans that they should NEVER meet:

Heatran, to protect mountains.
Moltres, to keep the world's insides, lava and molten rock, inside it.
Articuno, to guard over icy mountains.
Zapdos, to regulate global temperatures.
Raikou, to regulate the magnetic and gravitational forces of the world.
Entei, to keep volcanoes in check.
and Suicune, to keep the lakes and rivers in purest quality.
(Scientists now realize that Arceus created more than one of these above
pokemon as well, just not as many as common pokemon like Magikarp).

The Master then prepared for its holy rest with some final acts of creation:

Mew, to watch over the human race.
Jirachi, to sleep until the time was right.
Shaymin, to increase nature's beauty with flowers, trees, and berries.
Rotom, which later helped post-modern humans discover electricity.
And Celebi.

Celebi was given instruction to pull ideas for pokemon from Arceus' mind when the Master entered its prolonged rest. Satisfied with the universe, the Master ripped open a portal to Alternate dimension. But as the portal closed, two things fell out:

The Heaven's Pipe, for the greatest trainer to summon Arceus many thousands of years later, and:

Regigigas.

Regigigas summoned his three minions, Regirock, Regice, and Registeel, from
the other Plane, and they began to wage war against the humans. With their Pokemon and the Legendaries, the humans began a monumental clash with the Regi's. Soon, they noticed that Regigigas' power came directly from his minions. So someone cast a Spell of Estrangement on Regigigas, and soon he became slowed and finally, he stopped. The other Regi's blindly followed their master into a deep sleep. They all rejoyced, for the Regi's had been defeated.

But they made one mistake: The humans had no interdimensional portal, and thus the Regis were imprisoned on the Pokemon World, with the potential to awaken with a vengeance. So, they decided that yet another spell was to be cast. This spell would not only bind Regigigas to the temple in which he was held, but hold the others captive in three seperate, enormous mausoleums of stone so long as no one disturbed the Sealed Chamber, which was hidden beneath the sea.

After this, humankind lived in harmony with nature and pokemon for thousands of years. Celebi kept the flow of new pokemon going, Jirachi slept on, and Mew ensured that no human became too evil, and none did for thousands of years. Eventually the Pokemon of Mirage fell into slumber...

It was about then, thousands of years later, that Ash Ketchum woke up late for
his pokemon journey.

The rest of the story is told in the media and games: the story of Ash,
Pikachu, Red, Blue, Yellow, Green, May, Misty, Brock, Tracey, Dawn, Gary,
Paul, and the other trainers and leaders of the pokemon world, as well as that
of that of the Legendary pokemon, the Original Pokemon, and the many areas
known to scientists.

But Mostly that of the incredible discoveries of Professors Oak, Birch, Elm,
Ivy, Rowan, and many others, as they continue to find out more and more about
pokemon every day...

And Celebi helps them along with an endless flow of new Pokemon!

@ Trogdor: Did I forget to put in the part about how humans, in their greed for power, attempted to breed more Manaphy, but instead, they got the water faerie Phione? Oh well... Also, the Lati's weren't there at the beginning of Time. They were pulled from Arceus' dreams like so many other pokemon were.

@ Dustminion: No, it's exactly what it says it is: an ancient, much more... (what's the word? Useful!) version of Magikarp, before some unknown incident rendered it the most useless of Pokemon.

@ JDLJDL: Thought you'd like that part...