The Golden Compass is set in a universe that is parallel to our own. There, characters’ inner selves exist as physical companions that take the form of animals called dæmons. While children’s dæmons can freely change from one form to another, when a person becomes an adult his or her most prominent personality traits are manifested in a dæmon with a permanent form.
In this world, an authoritarian theocracy commonly known as the Church dominates society, suppressing people and ideas that it considers dangerous or heretical. The novel’s protagonist is Lyra Belacqua, a 12-year-old girl raised by scholars at Oxford University in England.
Lyra’s father, who she believes is her uncle, is the mysterious and powerful Lord Asriel. Her mother, who she has never met, is Mrs. Coulter. Lyra was born out of wedlock, and due to her parents’ position in high society, they were unable to raise her themselves. They left her to the care of the university, and Lyra does not learn of her true identity until later in life.
A few hundred years before the story begins, a Russian scientist discovers an elementary particle, similar to protons or electrons. This particle is given the name “Dust.” Both Lyra’s mother and father have been involved in high-level research regarding the nature of Dust, although this research is very sensitive because the Church only recently stopped denying the existence of Dust and included it in its doctrine.
Shortly after Lyra’s father embarks on a research trip to the North Pole, where Dust is more easily observable, Lyra’s mother arrives at Oxford. She is the leader of an organization called the Oblation Board which is secretly responsible for kidnapping hundreds of children across England and sending them to research centers in the North. While Mrs. Coulter is in Oxford, several children from the town, including Lyra’s best friend Roger, are kidnapped. Not knowing that Mrs. Coulter is responsible for the kidnappings, the Master of Jordan College sends Lyra away to be the woman’s assistant in London. Before leaving, the Master secretly gives Lyra an alethiometer, a small device that provides the true answer to any question—but only to those who know how to read it.
In London, Mrs. Coulter prepares Lyra to accompany her North on a research trip. Lyra is initially excited because she hopes to rescue her friend Roger. However, at Mrs. Coulter’s cocktail party Lyra overhears some adults discussing the woman’s responsibility for the kidnappings. She also hears that her father has been imprisoned on a far northern island called Svalbard, where he is being guarded by a group of intelligent armed bears called panserbjørne. She runs away from Mrs. Coulter’s apartment and wanders the unfamiliar streets of London until she is picked up by a family of gyptians that she knows from Oxford. Gyptians are a marginalized ethnic group that live on boats and travel up and down the rivers and canals of England.
The gyptians tell Lyra that many of their own children have been kidnapped and that they are on their way to an assembly of gyptians to organize a rescue party to the North. When they arrive at the assembly, Lyra meets John Faa, the leader of the gyptians, and Farder Coram, an elderly gyptian wiseman. They reveal that they have kept an eye on Lyra for her whole life. They also tell Lyra the true story of her birth as well as the identity of her mother and father.
John Faa is at first hesitant to bring Lyra north with him, but when he discovers that she has learned to read the alethiometer accurately, he decides that her presence on the dangerous mission is necessary. An army of gyptian volunteers sets out with John Faa, Farder Coram and Lyra on a ship to the far northern country of Norroway. In Norroway Farder Coram makes contact with Serafina Keppala, a centuries-old witch and queen of her clan with whom he had a love affair forty years ago. Lyra also enlists the help of Iorek Byrnison, an armored bear with opposable thumbs and human-like intelligence who has been exiled from bear society. Meanwhile, John Faa has hired Lee Scoresby, an American aeronaut who can help their effort with his hot-air balloon.
Having assembled their team on the coast of Norroway, Lyra, the gyptians and their companions once again head North. On the way Lyra finds a lost child whose dæmon has been severed from him. In this way, she learns what the Oblation Board does to the children they kidnap: At a far northern research station called Bolvangar, they perform a process called intercision that permanently severs the bond between a child and his or her dæmon.
Shortly after, a group of local hunters attacks Lyra’s caravan. They kidnap Lyra and bring her to Bolvangar, where they sell her to the Oblation Board’s team. While at Bolvangar, Lyra hides her identity from the adults in charge and begins to plot her escape. Knowing the gyptians are on their way, and with the support of Serafina Keppala’s dæmon, Lyra sets fire to the research station and organizes the children to flee. A battle ensues between Mrs. Coulter’s forces and the coalition of gyptians, witches and Iorek Byrnison who support Lyra. The gyptians manage to make it safely to the South with their children, while Lyra continues further North in Lee Scoresby’s hot-air balloon, accompanied by Serafina Keppala, Iorek Byrnison and Roger. They make their way to Svalbard, hoping to free Lord Asriel from his panserbjørn prison.
Arriving at Svalbard, the hot-air balloon is attacked and Lyra falls out. She is picked up by the bear king’s guards and imprisoned in his palace. She learns from her alethiometer that Iorek is on his way to save her, but that when he arrives the palace guards will gun him down for disobeying his exile. Lyra remembers hearing from a Scholar at Oxford that the current King of Svalbard wants nothing more than to have a dæmon. She tricks him into believing that she is Iorek’s dæmon and that if he defeats Iorek in a one-on-one battle, she can become his dæmon. The king believes her and orders his guards to allow Iorek to enter the palace. In the duel, Iorek defeats the bears’ king, killing him and becoming king himself. Shortly after, Roger arrives at the palace after following Iorek’s trail.
Finally, Lyra seeks to free her father from captivity and to give him the alethiometer, which she believes is her destiny. For this last part of her journey, Iorek Byrnison and her friend Roger accompany her. Lord Asriel is a cunning man and was able to convince his bear captors to imprison him in a large, luxurious house equipped with a library and laboratory. Lyra is surprised to learn that her father actually has little interest in the alethiometer. In reality, what he needed Lyra to bring him was a child, which she did unwittingly.
Finally reunited with her father, Lyra demands that he explain to her what Dust is. He tells her that the Church considers it to be the source of Original Sin. Scientists have observed that it is strangely attracted to adults once their dæmons take on their permanent form, but is hardly attracted to children at all. He explains that this is the purpose of intercision: to prevent a person from attracting Dust and thus prevent sinfulness. However, he believes that the Oblation Board has not gone far enough. He has discovered that Dust enters their world from another parallel world, and he desires to build a bridge to that world in order to find and destroy the source of Dust. Lyra has a hard time processing all of this new information, and her father sends her to sleep.
After everyone has gone to sleep, Lord Asriel awakens Roger and takes him away on a sled. Lord Asriel’s servant alerts Lyra and she and Iorek chase after them. Iorek takes Lyra as far as he can, but he must turn back when they reach an unstable bridge that cannot support his immense weight. Lyra says goodbye, and crosses the bridge alone. On the other side of the gulley, she continues to follow her father’s tracks. She catches up with her father and Roger, but not soon enough to save her friend’s life. Lord Asriel severs Roger from his dæmon, making use of the energy that is released in the process to build a bridge to the parallel world where Dust comes from. He walks across the bridge, and Lyra decides to follow him. She believes that Dust must actually be a good thing if so many evil people think that it is bad. She hopes to find the source of Dust before her father does and save it from being destroyed.