A thousand years ago, there were 3 beautiful sirens that roamed Equestria. They had the power to charm ponies with their music; but to maintain this power they had to feed off the negativity and distrust of others. The more of this energy they consumed, the stronger their voices became and the farther they can spread their dark magic. If the sirens had their way; they would have divided and conquered all of Equestria.
But a brave and powerful unicorn who goes by the name of Star Swirl the Bearded wasn't having any of it; and so found a way to banish the three to another world where magic doesn't exist. (As well as sending them 1000 years into the future) Little does he know that the world he banished them to was filled with powerful creatures that are more deadly than the monsters he'd seen in Equestria.
Days later; Star Swirl had a feeling that the sirens would strike again some day; and so he left his projects behind and followed them to learn the secrets of the Pokémon universe.