In an alternate Earth, a powerful church called the Magisterium strictly controls the populace's beliefs and teachings. In this world, every person's inner spirit partially exists outside the body, manifesting itself as an animal companion called a dæmon. The dæmon communicates with the person and must remain in close physical proximity. Witches, however, have bird-shape dæmons that are able to travel long distances from their bodies.
Lyra Belacqua, whose dæmon is named Pantalaimon or "Pan", is an orphan being raised at Jordan College in Oxford. Her uncle, Lord Asriel, a noted explorer and scholar, has been absent seeking the elusive Dust, a cosmic particle that the Magisterium forbids to be mentioned. When Asriel returns to Oxford, Lyra saves his life after seeing a visiting Magisterium agent spike his wine with an unidentified poison. Asriel later gives a presentation to other scholars regarding his discovery that Dust existing in the North Pole links infinite worlds. Asriel receives a grant for another expedition. If his theory is proven, it could severely undermine the Magisterium's control.
Lyra meets the wealthy Mrs Coulter, a "friend" of the college. She invites Lyra and invites to stay with her in retrofuturistic London. Before Lyra leaves, the Master of the college entrusts her with her uncle's alethiometer, a compass-like artefact that reveals the truth (the titular golden compass). Few individuals can decipher its symbols. The Magisterium has seized or destroyed all other alethiometers, and Lyra is warned to keep hers a secret.
Lyra notices the alethiometer continuously points to a symbol of a lady, a lightning bolt, and an infant, though she is unable to comprehend its meaning. Soon, Mrs Coulter's congenial manner changes and shows she is aligned to the Magisterium and its mandate. When Lyra casually mentions Dust, Mrs Coulter sternly warns her to never mention it again.
Kidnappers called Gobblers have been snatching poor, orphaned, and Gyptian children, including Lyra's friends Roger, an Oxford servant boy, and Billy Costa, a young Gyptian. Lyra later discovers that Mrs Coulter is head of the General Oblation Board and realizes they are the "Gobblers."
When Mrs Coulter's dæmon attempts to steal the alethiometer, Lyra and Pan escape with it into the streets. Gobblers pursue her, but she is saved by Ma Costa, Billy's mother. Lyra is taken to the Gyptian king, John Faa, whose ship is heading north to search for the captured children. A wise Gyptian elder named Farder Coram is able to decipher the compass.
After consulting with Magisterium agent Fra Pavel, Mrs Coulter sends two mechanical spy-flies after Lyra. One is batted away but the other is caught and sealed in a can by Farder Coram, who says the spy-fly has a stinger filled with a sleeping poison. Meanwhile, Lord Asriel has reached Svalbard, the kingdom of the Ice Bears, but he is captured by Samoyed tribesmen hired by Mrs Coulter.
The witch queen, Serafina Pekkala, tells Lyra the missing children are in an experimental station called Bolvangar. At a northern port, Lyra is befriended by a Texan aeronaut named Lee Scoresby. He advises her to hire him and his friend Iorek Byrnison, an armoured bear that Lee has come to rescue. Once a prince of the armoured bears, Iorek is now exiled in shame, the local townspeople having tricked him out of his armour. Lyra uses the alethiometer to locate Iorek's armour. After recovering it, Iorek joins the Gyptian trek northward, along with Scoresby.
Lyra, astride Iorek, goes to an abandoned building the alethiometer pointed her toward. There, Lyra finds Billy Costa, who has been surgically separated from his dæmon. The Gobblers are experimenting on the kidnapped children using a procedure called "intercision." Lyra reunites Billy with Ma Costa, but the group is attacked by Samoyeds, who capture Lyra. Iorek and Lee follow her in Lee's airship. Lyra is taken to the bear king Ragnar Sturlusson. Knowing Iorek will be outnumbered, Lyra tricks Ragnar into fighting Iorek one-on-one. Ragnar, who usurped Iorek's throne, initially appears to be winning; Iorek feigns weakness and kills Ragnar, avenging his father and regaining his kingdom.
Iorek carries Lyra to Bolvangar, but only Lyra crosses a narrow ice bridge before it collapses. Upon reaching the station, Lyra reunited with Roger. Lyra overhears Mrs Coulter telling the station scientists that Asriel escaped and has set up a laboratory. Magisterium soldiers are going there to arrest him for heresy. Lyra discovers scientists are experimenting to sever a child from their dæmon. Caught spying, Lyra and Pan are thrown into the intercision chamber but Mrs Coulter rescues her.
Mrs Coulter tells Lyra that the Magisterium believe intercision protects children from Dust's corrupting influence. She reveals she is Lyra's mother but was forced to give her up; Lyra realises that Asriel is her father. When Mrs Coulter wants the alethiometer, Lyra instead gives her the can containing the spy-fly. The fly stings Mrs Coulter, rendering her unconscious. Lyra destroys the machine, setting off a series of explosions.
Outside, the fleeing children are attacked by Tartar mercenaries and their wolf dæmons. Iorek, Scoresby, the Gyptians, and flying witches led by Serafina join the battle. The Tartars are defeated and the children rescued. Lyra, Roger, Iorek, Lee, and Serafina fly north to search for Asriel. Confirming Serafina's prophecy of an upcoming war with Lyra at its centre, Lyra is determined to fight the Magisterium, who plot to control all the other worlds in the universe.
Dakota Blue Richards as Lyra Belacqua, who embarks on a voyage to battle the forces of evil and rescue her best friend. New Line Cinema announced 11-year-old Richards' casting in June 2006.[5] It was her first acting role.[6]
Nicole Kidman as Mrs Coulter, an influential woman who takes an interest in Lyra (and later admits that she is Lyra's mother). Kidman was author Philip Pullman's preferred choice for the role ten years before production of the film,[7] and despite initially rejecting the offer to star as she did not want to play a villain, she signed on after receiving a personal letter from Pullman.[8]
Daniel Craig as Lord Asriel, Lyra's strict and mysterious adventurer uncle. In July 2006, it was reported that Paul Bettany was in talks to play the role.[9]
Sam Elliott as Lee Scoresby, a Texan aeronaut who comes to Lyra's aid. Pullman has singled out Elliott's performance as one the film got "just right."[10]
Eva Green as Serafina Pekkala, a witch queen.
Jim Carter as John Faa, the king of the Gyptians.
Clare Higgins as Ma Costa, member of a Gyptian family that aids Lyra.
Ben Walker as Roger Parslow, Lyra's best friend, who is kidnapped and taken north.
Charlie Rowe as Billy Costa, son of Ma Costa, and Lyra's friend.
Steven Loton as Tony Costa, son of Ma Costa and Billy's older brother.
Christopher Lee as the Magisterium's first high councilor. Lee's casting was also at New Line's behest, rather than that of Chris Weitz.
Tom Courtenay as Farder Coram, Gyptian second-in-command and advisor to John Faa.
Derek Jacobi as the Magisterial emissary.
Simon McBurney as Fra Pavel, a Magisterial agent.
Jack Shepherd as master of Jordan College.
Magda Szubanski as Mrs Lonsdale.
Edward de Souza as the Magisterium's second high councilor.
Paul Antony-Barber as Bolvangar Doctor.
Jason Watkins as Bolvangar Official.
Jody Halse as Bolvangar Orderly.
Hattie Morahan as Sister Clara.
Ian McKellen as Iorek Byrnison, an armoured bear (panserbjørn) who becomes Lyra's friend and comrade.
Freddie Highmore as Pantalaimon, Lyra's dæmon.
Ian McShane as Ragnar Sturlusson, king of the panserbjørne.
Kathy Bates as Hester, Lee Scoresby's hare (jackrabbit) dæmon.
Kristin Scott Thomas as Stelmaria, Lord Asriel's dæmon.
based on the 1995 book Northern Lights, the first novel in Philip Pullman's trilogy His Dark Materials.