Bookends: An interesting framing device is created by writing the epilogue first, where Carmodi explains her actions and motivations to the reader, none of which make sense (not even the reason for reversing the order of prologue and epilogue) until the prologue at the end of the book.
Taking the Bullet: Fitz, for the Doctor. Only it's a laser gun, and he survives with just a painful burn.
Timey-Wimey Ball: The three minions get somehow merged together when physics goes out to lunch near the end of the book, but don't manage to separate themselves before reality reasserts itself. The resultant terrifying monster evolves over time into an entire species: The Unnoticed, who have been chasing Carmodi and the Book of the Still the whole time.