The Subtle Knife by Philip Pullman

Lost in a new world, Lyra finds Will—a boy on the run, a murderer—a worthy and welcome ally. For this is a world where soul-eating Specters stalk the streets and witches share the skies with troops of angels. Each is searching—Lyra for the meaning of Dark Matter, Will for his missing father—but what they find instead is a deadly secret, a knife of untold power. And neither Lyra nor Will suspects how tightly their lives, their loves, and their destinies are bound together... until they are split apart.