Coulter and Lyra finally recognizes him as Lord Boreal from her world. Will and Lyra steal the alethiometer back, from Sir Charles-no small feat considering Sir Charles is being visited by Mrs. Will loses two fingers of his left hand in the fight. Will and Lyra return to Cittàgazze where they must fight for the knife, which has been stolen from its true guardian by the older brother of some of the children. He will only give it back in return for a knife in Cittàgazze. Will and Lyra go back to Oxford and Sir Charles steals the alethiometer. Mary Malone, a scientist who is working with what she calls Shadows. He tries to strike up a conversation, but Lyra is evasive and goes on to find Dr. In Oxford, Sir Charles, an older, obviously important and influential man, spots Lyra in a museum reading the alethiometer. The pair returns to Oxford, Lyra to search for a scholar who can answer her questions about Dust, and Will to find out information about his father.

Lyra shows Will her alethiometer, a compass-like device that is always truthful. Will and Lyra have stumbled into Cittàgazze, populated only by roving bands of children, two of whom have a secret about the Torre degli Angelica, the four-story tower in the middle of the town.

Lee Scoresby, the Texas aeronaut, is also looking for Lyra so he can protect her from the harm that so many mean to do the young girl. Serafina knew Lyra from adventures in the company of the bear-king Iorek Byrnison. The witch Serafina Pekkala, Lyra's rescuer from a cruel experiment designed to separate children from their daemons, is looking for Lyra. Will finds refuge in another world and meets Lyra who is searching for answers about Dust, a material that may be the cause of human consciousness. In trying to flee the thieves after he finds his father's letters, Will accidentally causes the death of one of the thieves. The book begins with Will Parry's efforts to keep his vulnerable and mentally unstable mother safe from two men who repeatedly harass them, demanding information about Will's vanished father, artic explorer John Parry. Will joins Lyra, the protagonist from the first book in the trilogy, and even though they have different goals and objectives at first, they discover that they are both an integral part of the same battle. This book introduces the character of Will Parry, a twelve-year-old boy who stumbles into another world by accident. The Subtle Knife is the second book in the three-volume His Dark Materials series and continues the story of the conflict between the Authority, personified by the Church, that demands humility and submission from all creatures and those who rebel against the Authority's control.

The Subtle Knife by Philip Pullman