The Subtle Knife by Philip Pullman (His Dark Materials #2)

Will is twelve years old and he's just killed a man. Now he's on his own, on the run, determined to discover the truth about his father disappearance.
Then Will steps through a window in the air into another world, and finds himself with a companion - a strange, savage little girl called Lyra. Like Will, she has a mission which she intends to carry out at all costs.
But the world of Cittàgazze is a strange and unsettling place. Deadly, soul-eating Spectres stalk in its streets, while high above, the wingbeats of distant angels sound against the sky. And in the mysterious Torre degli Angeli lurks Cittàgazze's most important secret - an object which people from many worlds would kill to posses.