The story starts where The Subtle Knife left off; Will is dealing with the aftermath of battle with the two angels, Baruch & Balthamos, Lyra has been kidnapped and drugged by her mother, Mrs Coulter, & the witch Serafina Pekkala has flown to find Iorek Byrnison and tell him of Lee Scoresby's death. This will all make a world of sense if you've read the first two in the series, otherwise it's about to get a whole lot more confusing.
The opening chapters cut between the different universes of the major players of the series, setting their paths to intersect in the future. Lyra and Mrs Coulter are in their own world in hiding in the Himalayas where Mrs Coulter is keeping Lyra drugged. However, each chapter while she is drugged ends with a dream sequence in which she talks to her friend Roger, who died at the end of Northern Lights, in the land of the dead. Meanwhile Will decides to pursue Lyra to be reunited, despite the angels pleading to take him to Lord Asriel to join his resistance. After narrowly avoiding an attack from Metatron, Balthamos stays with Will as protector whilst Baruch flies to share their intelligence with Asriel.
The main strand of the story is introduced in the happenings of the Consisterial Court of Discipline where the prophecy regarding Lyra is revealed - she has the role of Eve and central to the question of original sin. The Court decide to take action by sending Father Gomez as an assassin to kill Lyra. We are also introduced to Mary Malone's journey, who will take the role of The Tempter in the original sin story, leaving Cittàgazze and entering the world of the Mulefa.
As Will travels in search of Lyra in her own world, his path crosses with Iorek and the bears who arrive at the same port town. After Will ceases the fighting between the bears and the townspeople, Iorek agrees to travel with him to find Lyra. However, Lord Asriel's forces learn of a newly formed alliance between the Consisterial Court of Discipline & the Society of the Work of the Holy Spirit and that this force, in competition with themselves, are also racing to get to Lyra. Will snaps the knife trying to create a window to escape from the cave, so collects the pieces and, while a battle ensues between the forces outside, he and Lyra escape to another world.
Newly joined by two Gallivespian spies, Chevalier Tialys & Lady Salmakia, the children go back to find Iorek and get him to fix the broken knife. Iorek reluctantly agrees, fearful of the power of the knife, and affixes the pieces back together. He decides to move the bears back North to prepare for war, and Lyra & Will, with the Gallivespians in tow, hatch plans to go to the land of the dead.
In the search for the land of the dead, Lyra, Will & the Gallivespians arrive in a world where they find a dutch farm town recently ravaged by a military force. Finding the dead bodies of the inhabitants and hearing the boots of more soldiers they escape into a similar world that leads them to the suburb of the dead. Leaving Pantalaimon on the shores, for Daemons cannot cross into the land of the dead, the four make their way across the waters. Reaching the world, guarded by harpies, they find Roger, Will's father and Lee Scoresby, and negotiate with the harpies to free the ghosts with a window cut at the highest point in the land.
Following the cave, Mrs Coulter was captured by Lord Asriel and interrogated. She, however, escaped and made for the Consisterial Court, where she was arrested. Wit hthe help of Lord Roke, another of Asriel's spy, she escapes and finally works with Asriel.
The children exit into the world of the Republic of Heaven, where the final battle between Lord Asriel's forces and the forces of the Authority is in full swing. Mrs Coulter makes for the Clouded Mountain and tricks Metatron in following her to find Lord Asriel, and together she and Asriel pull Metatron down into the gap between worlds and cease to exist. Meanwhile, the Authority's weakened state meant that he was encased in crystal, and when freed by Will he dissolved into the air.
Will & Lyra collect their daemons and escape to the world of the Mulefas, with Will's daemon now taking physical form along with Pantalaimon. This final part is the prophecy realised; Will as Adam, Lyra as Eve and Mary as Tempter. The two children fall in love but after visits from Serrafina Pekkula and the angel Xaphania they learn the truth about the windows they create and realise they must return to their own worlds and close all but one window; the window from the land of the dead. They return to their own worlds and Will breaks the knife. They finally decide that every year, in order to be closer to one another, they will sit on the same bench in both Oxfords at the same time a year.