Yep, Ach is right. Shadows aren't really a part of the plot. Yet.

And yes, Ach is right, Shadow Lugia isn't responsible this time. Purified Pokemon can't be turned into Shadows again, so ultimately that theory is busted...

And aren't you forgetting a certain Legend that causes storms wherever it goes? The Hoenn-Native one that's a Water Type? Or Perhaps the one that causes superstrong sunlight where it happens to be, that Ground-typed one? :P