There's nothing better than a well-executed plot twist, especially when you're able to look back at the story and realize that you'd been given hints all along. What science fiction or fantasy story does this the best? (Warning: We're going to have to talk spoilers.)
My pick is the original Alien film, where we discover about halfway through the movie that the Weyland Yutani Corporation always intended for the unarmed, unprepared cargo vessel to pick up an alien specimen. We only find this out after the mortally wounded android character — whom we've actually come to trust — reveals his secret job was to protect the alien and basically let it eat all the humans if it wanted to.
So the movie goes from being a scary horror movie in space, to being a corporate dystopia about workers who are subjected to horror by their company. It adds another dimension to the film, and is a good surprise — though not entirely unexpected. Nice twist, well justified by a lot of foreshadowing about how poorly the company treats its workers.
What are your picks? Please include links, video, images — and a description of why it was a good twist that was justified. You can write about any kind of SF or fantasy, whether a game, book, comic, TV series or movie.