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, their destinies are bound together...until they are split apart.