Northern Lights / The Golden Compass
In Northern Lights (released in the United States and Canada as The Golden Compass), the heroine, Lyra Belacqua, a young girl brought up in the cloistered world of Jordan College, Oxford, and her dæmon Pantalaimon learn of the existence of Dust, a strange elementary particle believed by the Magisterium to provide evidence for Original Sin. Dust appears less attracted to the innocence of children, and this gives rise to grisly experiments being carried out on kidnapped children in the icy wastelands of the distant North by Magisterium-controlled scientists. Lyra and Pantalaimon journey to save their best friend Roger Parslow and other kidnapped children from this peril, with the aid of the panserbjørne (armoured bear) Iorek Byrnison, John Faa and Farder Coram, leaders of the gyptians, the aëronaut Lee Scoresby, and the witch Serafina Pekkala. During the trip, Lyra discovers the identity of her parents: Lord Asriel (ostensibly her uncle, who placed her at Jordan College and who has a daemon in the shape of a snow leopard) and Mrs. Coulter (who has a golden-monkey daemon). She loses any trust she had for Mrs. Coulter after she and Pantalaimon nearly become separated, or "cut" apart. Lyra succeeds in saving the children from the Gobblers (the General Oblation Board). After the children's dealings with armoured bears (Iorek returns from exile and wins back his Svalbard kingdom by killing the current king of the bears, who has become corrupt by wanting to be more human than bear) and witches and success in many arenas, Lord Asriel kills Roger in his own successful experiment to create a bridge into another world. Lord Asriel, followed by Lyra and Pantalaimon, journey through it separately in search of the source of Dust, unaware that they both mean to prevent the Magisterium from destroying it.

The Subtle Knife
In The Subtle Knife, Lyra journeys through the Aurora to Cittàgazze, an otherworldly city whose denizens have discovered a clean path between worlds at a far earlier point in time than others in the storyline. Cittàgazze's reckless use of the technology has released soul-eating Spectres, rendering the world incapable of transit by post-adolescents. Here, Lyra meets Will Parry, a twelve-year-old boy from our world who has stumbled into Cittàgazze after recently killing a man to protect his ailing mother in an effort to locate his long-lost father. Will becomes the bearer of the titular Subtle Knife, a tool forged 300 years ago by Cittàgazze's scientists of the same materials as the silver guillotine. One edge of the knife can create portals between worlds and the other edge easily cuts through any form of matter. After meeting with witches from Lyra's world, they journey on. Will finds his father, who has been lost in Lyra's world under the assumed name of Stanislaus Grumman, only to watch him murdered almost immediately, and Lyra is kidnapped by her mother, Mrs. Coulter, an agent of the Magisterium who has learned of the prophecy that Lyra is to be the next Eve. Will is then instructed by a pair of angelic lovers, Balthamos and Baruch, that he must travel with them to give the Subtle Knife to Lyra's father, Lord Asriel, as a weapon against The Authority.

The Amber Spyglass
In The Amber Spyglass, Will ignores the angels and with the help of a local girl named Ama, the Bear King Iorek Byrnison, and Lord Asriel's Gallivespian spies, the Chevalier Tialys and the Lady Salmakia, rescues Lyra from the cave where her mother has hidden her from the Magisterium, which has become determined to kill her before she yields to temptation and sin like the original Eve. They journey to the Land of the Dead, temporarily parting with their dæmons to release the ghosts from their captivity imposed by the oppressive Authority. Mary Malone, a scientist of the world of Will, interested in Dust (or Shadows, as she knows them), travels to a land populated by strange sentient creatures called Mulefa. There she learns of the true nature of Dust, existing as panpsychic particles of self-awareness. Lord Asriel and the reformed Mrs. Coulter team up to destroy The Authority's Regent Metatron, but are killed in the process, taking Metatron down with them. The Authority himself dies of his own frailty when Will and Lyra free him from the crystal prison Metatron has trapped him in, able to do so because the prison's protectors are killed or driven away in an attack by cliff-ghasts. When Will and Lyra emerge from the land of the dead, they find their daemons (Serafina names Will's soul, now in a daemon form, "Kirjava"). After all of this, Lyra loses her ability to read the alethiometer, and the book ends with Will and Lyra falling in love but realising they cannot live together in the same world; because all windows must be closed to prevent the flow of Dust, and because they can each only live full lives in the world they are born into. During the return, Mary learns how to see her own daemon, who takes the form of black Alpine chough.