The story takes place in an alternate world dominated by a powerful church called the Magisterium, and where part of the soul resides outside a person as an animal companion called a dÃ¦mon. Lyra Belacqua, an orphan raised in a college in Oxford, England, and her dÃ¦mon Pantalaimon (Pan) witness a Magisterium agent poison her uncle's bottle of Tokay. Lyra then warns her uncle, Lord Asriel, who instructs her to remain in hiding. Lyra watches Asriel give a presentation regarding Dust, a particle that the Magisterium has forbidden the mention of. The college gives Asriel a grant to fund a northern expedition.
At dinner, Lyra meets Mrs. Coulter, who insists on taking Lyra north as her assistant. Before Lyra leaves, the Master of the college entrusts her with the only remaining alethiometer, a compass-like artifact that reveals the truth. The Magisterium has destroyed all the others. He instructs her to keep it secret, especially from Mrs. Coulter.
At Mrs. Coulter's house in a city that resembles a futuristic London, Lyra mentions 'dust', a type of mysterious particle. This puts Mrs. Coulter on edge and she warns Lyra never to mention it again, and also insists that she leave the bag containing the aleithiometer. Mrs. Coulter's dÃ¦mon (a golden monkey) attacks Pan, causing Lyra to give in. Lyra and Pan discover that Mrs. Coulter is head of the General Oblation Board, the "Gobblers", who have been kidnapping local children. She also discovers that her best friend Roger and her Gyptian friend Billy have been taken by the Gobblers.
Lyra and Pan walk in on Mrs. Coulter's dÃ¦mon attempting to steal the alethiometer. They escape into the streets. The "Gobblers" pursue her, but she is saved by some Gyptians. Aboard a Gyptian boat heading north to rescue their children, Lyra shows the alethiometer to a Gyptian wise man, Farder Coram. On deck that night Serafina Pekkala, the witch queen, tells Lyra that the missing children are in a place called Bolvangar. Mrs. Coulter sends two mechanical spy flies after Lyra. Pan; one is batted away but the other is caught and sealed in a tin can by Farder Coram, who explains that the spy fly has a sting with a sleeping poison. Lord Asriel is captured by Samoyeds hired by Mrs. Coulter on his expedition but he bribes his captors into releasing him.
At a northern port, Lyra is befriended by a Texan aeronaut named Lee Scoresby, who advises her to hire an armoured bear. Exiled in shame, the giant polar bear Iorek Byrnison has been tricked out of his armour by the local townspeople. Using the alethiometer Lyra tells Iorek where to find his armour. Armoured again, the fearsome Iorek and his friend Lee Scoresby join the trek northward.
That night while riding on Iorek's back, Lyra finds a cowering and changed Billy separated from his dÃ¦mon Ratter. Lyra reunites Billy with his mother just as the group is attacked by Samoyeds who capture Lyra. Taken to the armoured bear king Ragnar Sturlusson, Lyra tricks him into fighting Iorek one on one. At first, Ragnar seems to have the upper hand in the fight, but Iorek eventually tricks his rival and kills him. He then becomes the new king. Iorek carries Lyra near to a thin ice bridge near Bolvangar. Reaching the station, Lyra is taken to eat with the missing children. While hiding again Lyra discovers that the Magisterium scientists, under the guidance of Mrs. Coulter, are performing experiments to sever the bond between a child and his or her dÃ¦mon. Caught spying, Lyra and Pan are thrown in the intercision chamber, and end up unconscious from the energy force that tries to cut them. On seeing Lyra in the chamber, Mrs. Coulter rescues her and takes her to her quarters.
When Lyra wakes up she is comforted by a distraught Mrs. Coulter, who explains the dÃ¦mon cutting to Lyra and also tells Lyra that she is her mother. Lyra then guesses that Lord Asriel is her father. When Mrs. Coulter asks for the alethiometer, Lyra gives her the can containing the spy fly. The fly stings Mrs. Coulter, knocking her and her dÃ¦mon out. Lyra runs to the room with the intercision machine. The growing chain reaction builds as Lyra yanks a control box loose and hurls it into the intercision machine, causing it to explode. This sets off a series of explosions that tear the facility apart.
Outside, the children are attacked by Tartar mercenaries and their wolf dÃ¦mons. The battle is joined by Iorek, the Gyptians, and a band of flying witches led by Serafina Pekkala. The Tartars are defeated and the children are rescued. Rather than returning south, Lyra, Roger and Iorek fly north with Lee Scoresby in search of Lord Asriel.
Unaware that he is in mortal danger, Lord Asriel has set up a laboratory to investigate the glowing Dust from another world.
Where did Lyra and Pan escape to?
The streets