"Years and years ago, there were two towers in Ecruteak. But one day, the western tower was hit by lightning and burned until the rain extinguished it, killing three Pokémon. So a rainbow-colored Pokémon descended from the eastern tower and revived the three, before leaving for lands unknown."

I'm summarizing, but that's the essential part of it. There are also mentions of another Pokémon from the western tower, but I've yet to find out more about it.