Used to express astonishment when somebody says or does something completely out of character. The only possible explanation is that they've been replaced by an alien shape-shifter who looks exactly like them, but acts differently.

The phrase is a parody of the cliché found in old movies, when somebody returns home to find their lover gone and a stranger in their place.
Shanee: "I'm going to stay in tonight and study."
Ruthie: "Who are you, and what have you done with Shanee?"
by Yogi Bhajan February 9, 2011