In a ruined and toxic future, a community exists in a giant underground silo that plunges hundreds of stories deep. There, men and women live in a society full of regulations they believe are meant to protect them.

Lyra is an orphan who lives in a parallel universe in which science, theology and magic are entwined. Lyra's 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 Lyra 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.