Scientists at CERN fired up the Large Hadron Collider and it created a rift in spacetime that sent two percent of people into a parallel dimension.

Or the Sudden Departure really turned two percent of people into dogs and two percent of dogs into humans, just as some obscure religion prophesized God would always do.

They could have come up with any sort of dumb shit to be the reason why the people disappeared and it wouldn't have added anything to the show.