Lyra has come to admire the works of two writers: Simon Talbot, a philosopher who asserts that rationality is all and that dæmons are a delusion; and the novelist Gottfried Brande who similarly denounces everything other than pure reason.

The murdered man is Roderick Hassall, a botanist, and the journal that of his colleague Dr Strauss who had been studying a commercially-important rose whose oil is connected to Dust.

Marcel Delamare, Lyra's uncle and an ambitious Magisterium cardinal, learns that rose oil allows people to see Dust.

Pan meets a young refugee named Nur Huda el-Wahabi who has lost her dæmon, and they decide to travel together to the Blue Hotel.

Lyra journeys across Europe and the East, following the addresses in Hassall's notebook and aided by supporters of Oakley Street as well as a loose collective of people who have been separated from their own dæmons.

Bonneville, who has been tracking Lyra, is about to shoot her when he is prevented by Ionides who advises him to "leave her alive for now" as she will be the key to a great treasure to be found three thousand miles to the East.

The novel ends with the words "To be concluded..." The Secret Commonwealth of the title refers to things that are outside the realm of rational thought, such as ghosts, fairies, and superstition.

[3] Pullman took the title from a 17th-century book of the same name by the Scottish clergyman Robert Kirk, about encounters of country folk with supernatural creatures.

[4] At the end of the text, Pullman notes that three character names are those of real people: Bud Schlesinger, Alison Wetherfield, and Nur Huda el-Wahabi.