The Secret Commonwealth

by Philip Pullman

During a nightly excursion, Pantalaimon witnesses a man being ambushed and murdered on the towpath. The two attackers search for luggage the man would have been carrying, but are unsuccessful. The man's dæmon flies to where Pantalaimon is hiding and asks him to come and help them. The man asks him to remove his wallet. Shocked that the man and his dæmon could also separate from each other, Pantalaimon witnesses their death.

Lyra and Pantalaimon examine the wallet; they find a left luggage ticket. At the railway station, they retrieve a rucksack from the locker, which contains numerous plant seeds and samples, a notebook of names and addresses, and the murdered man's diary. The diary details an expedition the man took to a mysterious, vast building in the middle of the deep desert of Lop Nor. Dæmons cannot pass through this desert as far as the building, requiring the man and those in his party to separate from their dæmons. The building is of supreme importance for the growth of a special strain of roses, the oil of which has numerous medicinal properties, including granting the ability to see Dust. Control of the roses is sought by both a range of powerful pharmaceutical companies and the Magisterium, who regard belief in the existence of Dust as heresy. According to the diary, a dying member of the man's party was successful in gaining entry to the mysterious building, but the rest of the group was turned away.

Lyra visits Alice Lonsdale, the former housekeeper of Jordan College, Oxford and learns that Alice is Malcolm's childhood friend. Alice and Malcolm tell of their journey to Oxford during the floods 20 years earlier and how they kept her safe. They return to find that her rooms have been ransacked and the rucksack stolen, but Lyra had already substituted the contents to keep them safe. Lyra and Pantalaimon, already barely on speaking terms, have an emotional argument when Pantalaimon reveals he recognised one of the names in the dead man's book but did not tell her. Pantalaimon reiterates that he believes Lyra's admiration of rational scholars has deadened her curiosity and enthusiasm for life, and Lyra angrily rejects his arguments by scorning all appeal to emotion. The following morning, Pantalaimon has left, leaving her a note reading: Gone to look for your imagination.

Distraught at Pan's absence, Lyra seeks help from the gyptians and joins her old friend Farder Coram in The Fens. He, like Malcolm, is an agent of Oakley Street, a department of the Secret Service. He arranges a safe passage out of the country and she leaves as Magisterium forces reach the gyptians. Lyra begins to make her way across Europe towards the Middle East in an attempt to find Pantalaimon, who she thinks may be trying to reach “the Blue Hotel,” a ruined city in the desert referenced in the murdered man's diary said to be inhabited by dæmons who have been separated from their humans. At the same time, Malcolm is dispatched by Oakley Street to find out more about the mysterious roses that only grow in the desert referenced in the diary. Rose growers of any kind, even those growing “normal” roses, are being terrorised and murdered by mysterious attackers from the mountains.

Marcel Delamare, Marisa Coulter's brother, an ambitious young cardinal, has been obsessively hunting Lyra. He is aided by Olivier Bonneville (son of Gerard Bonneville), a brilliant young scholar who has developed a new way to read the alethiometer without the cumbersome reference books usually required. The use of this new method can yield very specific results, at the cost of intense physical discomfort and nausea, it can only be used for questions about present events. Bonneville goes in pursuit of Pantalaimon, whom he finds is more easily tracked by his new reading method.

Pantalaimon arrives at the home of the author of the novel that has fascinated Lyra. The man is a recluse and has a strangely distant relationship with his dæmon. Pointedly ignored by the author, Pantalaimon leaves frustrated and disturbed. As he is about to leave the city, he is caught by Bonneville, and Bonneville is immediately arrested by agents of the Magisterium. Bonneville bluffs his way out of captivity only to find that Pantalaimon has escaped. Bonneville resolves to kill Malcolm, having learned that he was the one who killed his father. He catches up with Malcolm in Constantinople but is disarmed and defeated by Malcolm. Malcolm extracts information from him about Lyra's situation and the much-pursued rose oil, in exchange for information about Bonneville's past, though he maintains that he did not kill Bonneville's father. He lets Bonneville leave, and Bonneville sets out to track down Lyra.

Lyra arrives in Prague. An address listed in the dead man's book leads her to a bookseller who is sheltering a man who is continuously aflame: the result of an experiment carried out by his father, an alchemist and magician. The man's dæmon was transformed into living water by the same experiment, leaving them permanently unable to touch. His dæmon was subsequently stolen by his father, and the man pleads for Lyra's help recovering her. They track the alchemist down with the help of the murdered man's book of addresses, and the man and his dæmon are reunited, causing both of them to be destroyed. The alchemist reveals he had planned all of this from the beginning and needed the lethal burst of energy from their reunion to power one of his experiments. Horrified and reeling from the strangeness of this episode, Lyra berates the alchemist for his cruelty and indifference, but he speaks to her enigmatically, reveals himself to have been the burning man's father, and dismisses her. Lyra journeys towards the deserts of Syria, finding more and more refugees of the mysterious war being waged against rose growers everywhere. Pantalaimon meets a young refugee named Nur Huda el-Wahabi who has lost her dæmon in a shipwreck, and they decide to travel together to the Blue Hotel.

In a city near the edge of the desert, Lyra discovers a secret black market selling separated dæmons to humans in need of them, to allow them to pass in normal society. The author Pantalaimon visited is revealed to have bought a dæmon from a dæmon-seller here, explaining his strange relationship with his dæmon. Lyra locates a guide who takes her to the Blue Hotel, which she enters alone. Bonneville, who has tracked her, is stopped from killing her by Lyra's guide, who tells him that Lyra will lead them both to an unspecified treasure of incredible value, in Lop Nor. At the ruins, Lyra is greeted by Nur Huda, who tells her that "we have been waiting for you."