Hiya,
According to WPM posts on the main page, there's a story behind all the Delta Species...I'll try to summarize it.
Delta Species set: There a place called Holon, where people live normally(Lass, Farmer, Mentor) together with Pokemon. The Pokemon are DNA altered by Holon Scientists and Researchers at Holon Research Tower. These is basicly the introduction of Delta Species...
Holon Phantoms: While live peacefully with the Delta Species, there is one place, (I'm guessing Holon Lake or Holon ruins) where Delta Pokemon that hates normal Pokemon, like Mewtwo, because he is a clone. They made a place for themselves, like again, Mewtwo, as 'shadows', hence the name Holon Phantoms.
Crystal Guardians: There are also Pokemon that lives in Crystal Beach,(I know from the pictures of Kingler d picking up Crystals from the ocean) that lives together with normal Pokemon. There are alot of Crystals in Crystal Beach, which they guard, so no other people can take it from them. (The crystal have some special effects I guess, like the Crystal Shard and Seal Crystal). They live happily together...
The story continues with Furthest Ends of Offense and Defence sets, which I guess they all we start fighting for their rights of Holon.
Of course, this is only my made up story using info by WPM. =p
Probably true though..(Or close enough)
cya!