Thousands of years ago, someone predicted that Bod (or kid a lot like Bod) would destroy the Jacks. Because of this prediction, we can’t help but look at The Graveyard Book in terms of fate and free will. Was Bod destined to defeat the Jacks, or did he make choices in his life that led to his face-off with them? (If you've read the Harry Potter books, this is like the question of whether Harry is fated to defeat Voldemort or be killed by him.) Almost everything in Bod’s life seems specially arranged to prepare him for his battle with the Jacks. But, the decisions he makes throughout the novel are all his. His will is so strong, he sometimes goes against what his parents and guardians want. The novel might be saying that life is a funny combination of fate and free will, and that if we use our free will, we’ll be on track with our destinies.
Bod is very stubborn; because no one makes his choices for him, he’ll always be accepting his true destiny.
The prophecy is just a fantasy made up by the Jacks; if they had just left Bod alone, he wouldn’t have needed to kill the Jacks or even cared about them.