Yep, witches are actually aliens. Surprised? In Doctor Who, they are explained away as a race of aliens called Carrionites who can manipulate time and space with their vocal waves. For the uninitiated, this means spell-casting. Essentially, this is explained as a word-based science that uses certain vibrations and sounds of words to reshape reality. Why are they so ugly? Because they're not actually very human-looking. To look human, they have to cast yet another spell, which drains a lot of energy. Those able to maintain that energy actually look quite beautiful. It's when that energy begins to dissipate that you get the classic snaggle-toothed hag.
