Story
At the Spear Pillar, Arceus has called a meeting for all legendaries to attend. The discussion was how humans are trying to capture them and use them for selfish needs. More human societies are being built and more forests destroyed. Some of the pokemon had nowhere to go and were just captured by the evil humans. The world was no longer safe for pokemon, Arceus concluded. They needed a plan, and Giratina had one: Human extermination. The legendaries were appalled and greatly disagreed with Giratina's solution. Then Palkia came up with the perfect solution: He would create a new world just for pokemon. The legendaries agreed this was the perfect solution.
Suddenly Xatu came to Arceus with a prophecy, "The reflection of the shadow will rise, as worlds collide. And the rainbow orbs will bond the souls of the stone bearers with the fate of the world." Arceus didn't know what the prophecy meant... But Xatu also foresaw a war with Arceus at the head. Arceus said that must be false. But it must have been true.
So Palkia created the planet Palestia and all the pokemon who wanted to leave came to the new planet, others stayed. But Giratina was sent to the reverse world in Palestia. But right as he got there, a shadow cloud engulfed him and turned him completely evil. He plotted to start a war and it was some select humans' destinies to stop the war. But in order to get to the world, the humans were turned into pokemon. But they had all of their human memories, but no clue why there were there or why they were pokemon.