When Malcolm finds a secret message inquiring about a dangerous substance called Dust, he finds himself embroiled in a tale of intrigue featuring enforcement agents from the Magisterium, a woman with an evil monkey daemon, and a baby named Lyra.

Twenty-year-old college undergraduate Lyra is once again thrown together with Malcom Polstead, now a professor, after Lyra and her daemon, Pantalaimon, receive secrets from a dying man about a daemon-haunted city and the origins of Dust.