In the beginning, there was Arceus. He sought to bring about existence, and created both Time and Space. To govern time, he created Dialga and to govern space, he created Palkia. A shadow of his new existing realm came to be, and so Arceus gave sovereignty of it to another creation, Giratina.
To inhabit the new existence, Arceus created galaxies and planets. Arceus went to one planet and made it his throne. For his throne, he created day and night. He created Cresselia to bring the day, and Darkrai to herald the night.
To inhabit and bring beauty to his realm, Arceus desired life to flourish and set on the creation of the sky, the land and the sea. To watch and guard the skies above, he created Rayquaza. To give life to the land, he created Groudon. To give life to the seas, he created Kyogre.
Arceus wanted the lands to be spread all over his world, and created golems to move them: Regigigas separated the many lands. Regice moved the polar caps to the north and the south. Regirock created the mountains and hills on all of the different lands, and Registeel created the valleys. Eventually, the lands were as Arceus willed them, and the golems retired to sleep.
To create life, Arceus gave the most of himself to Mew. Mew spread and created Pokémon and Humans. All were dumb, desireless, and emotionless, and so Arceus gave of himself to create Uxie, Azelf and Mesprit. Uxie was to bring knowledge, Azelf to bring will power, and Mesprit to bring emotion. The three spread and did their duties, and Pokémon and man became truly alive.
The first war came to be between Groudon, who was trying to spread more land, and Kyogre, who was trying to spread the sea. This taught man and Pokémon violence. Arceus was furious, and chained the will of Groudon and Kyogre to two separate spheres. Rayquaza was given the power to disable either of the two, and he became their guardian.
A new master of the sky and master of the land were needed, and so Arceus created Ho-oh and Lugia. Ho-oh created Entei to control the volcanoes, as they were a way for the land to be recycled. Ho-oh then created Suicune, to purify the waters of the world. Lastly, Ho-oh brought forth Raikou to guard the storms, which would clean the skies. Lugia created Articuno, Zapdos and Moltres to be the guardians of the world.
Arceus then brought forth Celebi, to be the ferryman of time should the need ever arise. He created Manaphy to be the prince of the seas and all of its treasures, as well as Shaymin, to be the prince of the land and all of its treasures.
Arceus grew tired, his abilities stretched beyond what he expected. He placed his will in his final creation, Jirachi, so that the needs of his sons and daughters could be answered. Arceus then went into slumber, so that one day he could return in full power.
Fast forward to the present:
"Jirachi, I wish that one day, man could become as powerful as the original Pokémon themselves…"