In order to rescue his criminal father and restore the family fortune, Artemis Fowl II and his trusted servant and bodyguard Domovoi Butler seek the existence of fairies (believing that it makes a connection to his father) in hopes of robbing 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.

14th-century knights transport a suspected witch to a monastery, where monks deduce that her powers could be the source of the Black Plague.