It's another one of this world's... quirks. It doesn't happen often, but it seems that every year or so, people get transported, powers return, and new people find themselves here. There's no explanation as to why it happens.

[ Again, another thing that can't be properly explained about Johto. Xion watches Xemnas' Pokemon for a moment before moving her gaze back to her former boss. ]

I've already been to The World That Never Was just now.