Lyra is an orphan who lives in a parallel universe in which science, theology and magic are entwined. Her search for a kidnapped friend uncovers a sinister plot involving stolen children and turns into a quest to understand a mysterious phenomenon called Dust. She is later joined on her journey by Will, a boy who possesses a knife that can cut windows between worlds. As she learns the truth about her parents and her prophesied destiny, the two young people are caught up in a war against celestial powers that ranges across many worlds.

15 year old Mattie has vivid dreamlike premonitions, which she is encouraged to ignore by her older brother Marco. But Mattie begins to sense that these visions might have more substance than they would like to believe.