Someone recently asked me about a plot twist in Albion Academy regarding Mrs. Pendragon. "Was that always the plan?" he asked. "At what point in the process did you know that was going to happen?"
That particular twist (if you've read the book, you know which one) actually came into the story very early on. Once I'd established that my Merlin was not THE Merlin, but instead his descendant, I quickly had the idea of his origins. Vivienne's nature, motivations, and role in the plot came with Merlin's. Sometimes plot twists are like that. They weave themselves into the plot so early on that they are like fixed points in time. The author knows they're coming the whole way through. Endings like that of The Thief can't really be written if they aren't supported in the whole of the book, and the process for those sorts of books goes much more smoothly if the author knows the ending in advance.
Other times, though, the twists can surprise the author as much as the reader. Tolkien famously wrote that when he got to the point in The Lord of the Rings when Frodo and the other Hobbits reach Bree, he had no better idea who Strider was or where Gandalf was than Frodo. For Albion Academy, Bryn's deal with Odin and Kaya's parentage were more surprises for me, coming much later in the process than Merlin's origins and Vivienne's motivations.
Even Albion Apparent has had its own surprises to throw my way. Mortimer's journey has taken some unexpected turns, James Corvin has revealed some character traits I never suspected, and Gabriel Faust continues to be one of the most interesting characters to write because of his unique perspective on the whole of Albion Academy.
What are some plot twists that took you by surprise?