NeoWolf has the right idea, I probably should have edited it to show how I worked.
Many years ago, in an idyllic world, all of the creatures lived harmoniously.
However, this utopia was shattered when suddenly, in the middle of a dark forest, a red gem materialized, corrupting all of the Pokèmon inhabitants with its evil influence.
Fire Pokèmon set parts of the forest ablaze, Flying Pokèmon began to consume Bug types, while Ground types began to summon earthquakes…
Celebi, the forest’s protector, attempted to end the chaos, but it ultimately failed, disappearing shortly after.
Humans began to worry after the forest’s guardian disappeared, and attempted to remove the gem that had caused the decline of the once peaceful world.
Unfortunately, no one even found the gem, and so they despaired.
Until, that is, a caped mystical man appeared from the Johto region, claiming that he was the Dragon Master, and that he would solve their problems by destroying the red gem.
The people laughed at his statements, jeering that he would not return, however, his unprecedented courage allowed him to go through the forest and locate the vile jewel. Unfortunately, none of his attempts to destroy it worked. Knowing that the others would taunt him if he couldn’t destroy it, he summoned his mighty Gyrados, commanding it to eat the gem.
As soon as this happened, the world returned to the way it was before the gem’s corruption.
Everything, that is, apart from the Dragon Master’s Gyrados, who's once blue scales turned crimson, as the Pokèmon became ill.
The man recalled the leviathan to its Pokèball, and ran out of the forest, desperate to find a Pokèmon Center. While the nurse healed the Gyrados to the best of her abilities, after it regained its strength it became uncontrollable.
Destroying the Pokèmon Center, it fled to the forest, and its trainer took chase. As he ran, he saw a scene that would never leave his memory: Celebi had returned, and halted the Gyrados’s onslaught with a mysterious red scale. Seeing the Dragon Master, it bestowed to him the scale, a reward for rescuing the
forest. Finally, it was saved.
Five centuries later, three more gems appeared in the region of Kitaura.
One in a lake.
One in a cave.
One... in a forest.
Hopefully that will give you an idea of what I can do.