A long, long time ago, there was a dark void known as The Darkness Of The Unknown. Out of it came a single, lone egg; which hatched into Arceus: The Pokemon Of Creation. Seeing this chaos, Arceus created two Pokemon, Dialga: The Pokemon Of Time, and Palkia: The Pokemon Of Space. Dialga spun time and Palkia expanded space. As Dialga and Palkia worked hard, Arceus created Uxie: The Pokemon of Knowledge, Mesprit: The Pokemon Of Emotion, and Azelf: The Pokemon Of Courage. Also, Arceus created Darkrai to tame The Darkness Of The Unknown and Cresselia to provide rest to the Pokemon when they are tired.
Seeing that it's creations needed a place to rest, Arceus created Groudon to create landmass, Kyogre to create water, Rayquaza to create a breathable atmosphere, Regirock, Regice, Registeel and their leader, Regigigas, to create continents, Mew to provide more kinds of Pokemon, Shaymin to create plants so the other creatures can eat the plant's berries, Heatran to provide heat for volcanoes and sea vents, Manaphy and Phione to monitor the oceans, and Deoxys to warn the others about incoming comets and asteroids that may wipe out forms of life. One day, an asteroid struck the planet.
Arceus and it's crew survived the blast, thanks to Deoxys' prior warning. Alas, when they got out of their cave, they saw death and destruction everywhere they went. Out of despair, Arceus created Giratina to guide the wandering souls to where they will have their final judgements. Also, Arceus created Raikou to create storms, Entei to provide heat to fuel storms and wildfires, Suicune to provide clean drinking water to plants and others, Ho-oh to create rainbows, Lugia to create ocean currents, Articuno to create cool seasons, Zapdos to create mild seasons, and Moltres to create warm seasons.
When Arceus learned that the time of man was coming soon, Arceus told Uxie to spread knowledge, Mesprit to spread emotion, and Azelf to spread courage when mankind comes to existance. Also, Arceus created Celebi to teach humans the origins and the history of the planet, Jirachi to make some of mankind's dreams come true, the Unown to help humans learn how to read and create different kinds of languages, and Latios and Latias to guard the first cities. Humans learned from Pokemon and vice versa for many millennia.
When humans got to the computer age, they revived Pokemon that were once extinct like Kabutops and Rampardos for example. Also, the humans created the Porygon line and Castform. All but one Pokemon the humans revived or created were tamed. It's name is Mewtwo. Mewtwo is the first Pokemon to be cloned and genetically engineered from Mew's fossil DNA, but the humans made it strong enough to defy them and Arceus. The Mewtwo then challenged Arceus to a battle. After a long, harsh battle, Arceus won the battle. Arceus punished Mewtwo by imprisoning it into a dangerous cave in Kanto. Then, Arceus said to the humans:
"If you manipulate my design, your kind shall be manipulated as well."
After saying those words, Arceus took to the skies and into space and was never seen again.