After the events of The Subtle Knife, we open on a cave nestled deep in the Himalayas, were Mrs. Coulter has hidden Lyra and is keeping her in an unconscious state using potions. While she sleeps, Lyra dreams of her childhood friend Roger, who is trapped in the world of the dead, and promises she will come for him. A young girl named Ama discovers the cave and brings food to Mrs. Coulter, but after discovering Lyra, plans to find some way to awaken her.
Meanwhile the angels Baruch and Balthamos are trying to convince Will to come with them to meet Lord Asriel, so that Will can use the subtle knife to kill God, who they refer to as the authority. Will refuses, stating that he first must rescue Lyra, and soon after the group is attacked by Metatron (the voice of God and strongest of the angels). Will manages to rescue the angels, and they escape into another world, whereupon Balthamos decides to accompany Will and Baruch returns to Lord Asriel’s side to inform him of Will’s refusal. On his way to the fortress, Baruch is attacked and mortally wounded, dying soon after informing Lord Asriel of Will’s possession of the knife an Lyra’s kidnapping. Lord Asriel gathers his allies an plans to rescue her.
The witch Serafina Pekkala contacts the king of the armored bears Iorek Byrnison to inform him of their mutual friend, aeronaut Lee Scoresby’s death. Iorek goes to retrieve his friends’ body from the world where he fell, returning to his own world and gathering the armored bears to press south to the Himalayas and rescue Lyra. While numerous groups hunt for Lyra, the mysterious Church has set its own misson. They have discovered through studying the alethiometer that Lyra is to be the new Eve, and the Church leaders have decided to kill her. They send a priest named Father Gomez to locate physicist Mary Malone, a former ally of Lyra’s who they believe will lead them to her. Additionally, they dispatch their own group to attack the Himalayas.
Mary herself is traveling through the alternate universes. She eventually comes upon one inhabited by the Mulefa, strange if intelligent beings that use wheels for mobility. They get along well and the Mulefa take her in and teach her their language. In Lyra’s world, Will and Balthamos (who is passing himself off as Will’s daemon) are still searching for Lyra. They come across Iorek’s group of armored bears, and Iorek agrees to take Will with them to rescue their friend. Additionally, two of Lord Asriel’s spies, Gallivespians Chevalier Tialys and Lady Salmakia are traveling with the Church group sent to attack the Himalayas.
Upon arriving in the mountains, Will encounters Ama, who quickly agrees to team up and rescue Lyra. They enter the cave using the subtle knife, but are caught by Mrs. Coulter, causing Will to break the knife before Chevalier Tialys stings and paralyses her. The Church and Lord Asriels forces converge on the caves and begin to fight, while will and Ama wake Lyra and bring her to safety. The two Gallivespians accompany them and they meet up with Iorek, who is fortunately able to repair Will’s knife. Lyra and Will decide that they will then go to the world of the dead to rescue Roger and the other souls trapped there. In order to do this, they must leave behind their daemons, and Will is surprised to discover he actually has one.
After a long and perilous struggle, they pass through the world of the dead and lead the ghosts to freedom, where ghosts like Lee and Roger can finally be reunited with their daemons. Mrs. Coulter meanwhile, has been captured by King Ogunwe, an ally of Lord Asriel. He brings her to Lord Asriel’s fortress, whereupon she steals a ship and flies to a branch of the Church known as the Consistorial Court, only to discover a plot to build a bomb to kill Lyra. Back in the Mulefa world, Mary has created a mirror that allows her to ‘see’ dust, thus creating the ‘amber spyglass’.
In the world of the dead, the Church’s bomb does indeed go off, but fails to kill Lyra, instead opening up a massive abyss. Will uses his knife to cut a path for the dead to escape through, and the ghost of his father informs him that his and Lyra’s daemons are hiding in Lord Asriel’s world, before escaping himself. Lyra and Will go to Lord Asriel’s world, where Metatron and his army are attacking his fortress. Lyra and Will encounter God and manage to rescue him from a group of cliff ghasts, but God dies shortly after, his form dispersing and drifting away into the atmosphere. The children then find their daemons and escape into the world of the Mulefa, and Mrs. Coulter lures Metatron to the edge of the abyss, where she and Lord Asriel drag him down, and the three perish together.
In the Mulefa world, Lyra and Will discover their daemons have disappeared again. The Mulefa bring them to Mary, who tells them about the slow disappearance of dust and explains to them a bit about what it is to fall in love. Will and Lyra come to realize that they are in love, but before they can affirm this with a kiss, they are attacked by father Gomez. Luckily, Balthamos appears and kills him.
As Lyra and Will came to the realization that they were in love, the dust stopped escaping so quickly, and their daemons return and settle into their final forms. Serafina Pekkala speaks with an angel named Xaphania, and the two agree that Will and Lyra must go their own way, due to the dust escaping through the anomalies caused by the subtle knife. They must return to their own worlds, and seal any doorways left open. Lyra and Will are distraught, and Lyra attempts to consult the alethiometer for another solution, but she has lost her natural ability to read it.
The no-longer-children agree to be separated, but they choose a spot that exists in both of their worlds where they can sit and think about each other in order to feel connected across dimensions. Will and Mary return to their world, and Lyra returns to Oxford and Jordan College, where she encounters a woman who offers to teach her how to read the alethiometer again. Lyra and her daemon, Pan, agree that they have to make the most of their life, no matter what world it takes place in, and they set about rebuilding a new and better world.
