Mrs. Coulter is keeping Lyra in a cave in the Himalayas of Lyra’s own world. She feeds Lyra a sleeping potion to keep her unconscious. A little servant girl named Ama decides to figure out a way to wake Lyra up. She gets a special powder from a local magician and brings it to the cave. Ama realizes that Mrs. Coulter is an evil woman. Lyra dreams she is speaking to Roger.Back in the world of Ci’gazze, Will and two angels, Balthamos and Baruch, argue over what to do. Balthamos and Baruch, who are lovers, come from a low order of angels. They insist that Will come with them, but Will says he has to find Lyra. Baruch flies ahead to look for her, and Will and Balthamos make their way down the mountain. Will and Balthamos enter Lyra’s world and Balthamos agrees to pretend to be Will’s daemon so that Will won’t stand out. Baruch returns, having discovered where Mrs. Coulter is holding Lyra. Suddenly, Metatron, the Lord Regent of God’s angels, attacks Will and the two angels, but they are able to escape. Balthamos tells Will that angels are made out of Dust. He also tells Will that God was not the creator of the universe, but was rather one of the first angels. When he gained power, he started telling the other angels that he had created everything. Another angel eventually found out the truth, so God banished her and all the angels that followed her. God is old now and Metatron rules in his place. Baruch decides to go to Lord Asriel and talk to him. Balthamos agrees to continue pretending to be Will’s daemon in Lyra’s world and to help Will find Lyra. In Lyra’s world, the climate is changing because of the rip in the sky that Lord Asriel made. Serafina finds Iorek Byrnison and tells him that Lee Scoresby is dead. Iorek finds Lee’s body and eats it. Then he returns to his own world to lead the bears south to the snowy Himalayas, as the bears’ own icy kingdom has been melting. Baruch approaches Lord Asriel’s fortress, the Adamant Tower. Two of Metatron’s angels attack him, almost killing him. Baruch is brought before Lord Asriel. He tells Lord Asriel that God now lives in a crystal chamber inside his roaming castle (which is called the Chariot or the Clouded Mountain) and that Metatron is the one who actually rules. Metatron no longer trusts the Church and wants to intervene directly in the lives of human beings in every world. Metatron and Baruch were men once—and they were brothers. Metatron banished Baruch.
Before dying, Baruch tells Lord Asriel where Lyra is and where Will is heading. Lord Asriel summons several of his allies, including King Ogunwe, an African king, and some Gallivespians. The latter are tiny people with poisonous spurs on their heels who ride hawks and dragonflies. The Consistorial Court (an arm of the Church) finds out where Lyra is. They know that she is to be the new Eve, so they send a force of soldiers to kill her. They also send out a lone assassin, Father Gomez, to follow Mary Malone. They hope that even if their mission to kill Lyra fails, Mary will lead Father Gomez to Lyra.
Mary Malone has made her way into another world from the world of Ci’gazze. She meets the mulefa, strange people who have trunks like elephants, diamond-shaped bodies, and claws that they hook through wheel-shaped seedpods. The mulefa befriend Mary and take her to their town. In Lyra’s world, Will and Balthamos are traveling together when Balthamos suddenly senses that Baruch has died. He panics, but Will convinces him to continue pretending to be Will’s daemon. As they travel toward the cave in which Lyra is being held captive, Will and Balthamos run into Iorek Byrnison and the armored bears, who are fighting with a town of humans. Will makes peace between the two sides and convinces Iorek, who is fascinated by Will’s knife, to allow Will to travel with the bears as they head for the Himalayas. Will tells Iorek that he is looking for Lyra and Iorek agrees to help Will in his search. Mary learns to communicate with the mulefa. She consults the I Ching, a Chinese method of fortune telling akin to the alethiometer. It tells her to stay with the mulefa for a while. A flock of tualapi, vicious white birds similar to swans, attacks the mulefa village, destroying it and scattering the precious seedpods. In Lyra’s world, Ama meets Will and Iorek and brings Will to Lyra. Will meets Mrs. Coulter for the first time. Mrs. Coulter explains that she is keeping Lyra asleep in the cave because she wants to protect Lyra from the forces of the Church. Will knows that Mrs. Coulter is lying and he leaves. Aboard the zeppelin of the Consistorial Court, the two Gallivespian spies hatch their special dragonflies. Through a device called the lodestone resonator, they receive a message from their chief, who tells them to cooperate with Will in order to save Lyra. Will and Ama use the knife to enter the cave in which Mrs. Coulter is holding Lyra. They wake Lyra using medicine that Ama obtained. Before they can use the knife to cut through to another world, however, Mrs. Coulter looks at Will, and he thinks he is looking at his own mother’s face. His heart fills with sorrow and the knife lodges in the air and breaks into pieces. The Gallivespian spies rescue Will and Lyra from Mrs. Coulter. Lord Asriel’s forces, commanded by King Ogunwe, meet the forces of the Consistorial Court and a great battle ensues. The Consistorial Court’s army retreats, and King Ogunwe captures Mrs. Coulter and brings her back to Lord Asriel. The spies insist that Lyra and Will bring the knife to Lord Asriel, but they refuse. They go to meet Iorek, who agrees to mend the knife. Will and Lyra decide they have to go to the world of the dead, because Lyra has to find Roger and Will has to find his father. In Lord Asriel’s fortress, Mrs. Coulter meets with Asriel and his allies. King Ogunwe explains to Mrs. Coulter that Asriel and his allies want to build a Republic of Heaven. Mrs. Coulter steals an airship called the Intention Craft from Lord Asriel and flies away. Lord Roke stows away with her. Mary Malone has become very close to the mulefa, especially to one zalif (the word for a single mulefa) named Atal. Mary learns that the mulefa can see Dust, or Shadows, which they call sraf. Atal tells Mary that the mulefa have existed for 33,000 years, and that the Dust comes from the mulefa themselves and the oil from their seedpod wheels. According to mulefa lore, 30,000 years ago, a snake told a female zalif to put her claw through one of the seedpod wheels and coat it with oil. When the female zalif obeyed, she was able to see sraf. The female zalif had her mate, a male, put his claw through the hole in a seedpod, and at that moment consciousness came into existence for the mulefa. Mary decides to make a mirror with sap from the trees so she can see the sraf as well. The technique works, and Mary can see that sraf surrounds adults much more than it does children. Sraf looks like golden dust motes in sunshine. Atal takes Mary to speak to Sattamax, the wisest of all the mulefa.
Sattamax asks for Mary’s help. He says that 300 years ago, the seedpod trees started to sicken. Without the seedpods, the mulefa cannot produce more sraf, and without sraf, they will go back to being dumb beasts. Mary agrees to help.
Lyra, Will, Chevalier Tialys, and Lady Salmakia make for the world of the dead. They cut through to another world and follow a group of dead people until they find themselves in a strange, colorless town. The dead are allowed to cross a river, but Lyra’s group is not allowed to cross. They have to seek shelter in a shantytown filled with people who are accompanied by death instead of daemons. Death is a shadowy figure that accompanies each person through his or her life until it is time for that person to die. Then death takes the person away. Back in the world of the mulefa, Mary builds a rope ladder to get to the top of the seedpod trees. The mulefa have turned Mary’s mirror into a kind of telescope, and with it, Mary can see thatsraf is not fertilizing all of the flowers. The mulefa build a platform in the tree canopy so Mary can learn more. In the world of the dead, Lyra, Will and the Gallivespians approach the river that only the dead can cross. The man who rows the dead across in a boat tells Lyra that Pantalaimon can’t go across the river. As the boat pulls away, Lyra feels Pan being torn away from her heart. Will and the Gallivespian spies feel tearing in their own hearts as well. The boatman leaves them on the other side of the river, where harpies attack them. Will, Lyra, and the Gallivespians flee and find themselves in a valley, surrounded by whispering ghosts. They are in the land of the dead. The ghosts tell Will and Lyra that when living things die, they end up in this dull valley where nothing ever happens, and the harpies tell them every bad thing about themselves until they lose all hope.
Lyra is appalled by the world of the dead. She decides that it is not enough to find Roger: she must free all the dead from the valley. As she is convincing them to follow her, a ghost who was a religious zealot while alive steps forward and says that this valley is actually Heaven, and that Lyra and Will are emissaries from the Devil who have come to lead the dead into Hell. The ghosts and the Gallivespians locate Roger and bring him to Lyra. Lyra apologizes to Roger for leading him to his death. While Will and the Gallivespians are conceiving of a plan to free the dead, Lyra comforts the ghosts with stories of her life in Jordan college. The harpies listen. Lyra and Will tell the harpies that they will make the dead tell stories. The harpies can feed on the stories of people who have lived full lives instead of on the spirits of the dead. In exchange for the stories, the harpies will lead the dead to an exit created by Will. With the dead trailing behind, the harpies lead the children and the Gallivespians to the highest point in the world of the dead. In Lyra’s world, Mrs. Coulter flies the Intention Craft to the Consistorial Court where she meets with Father MacPhail, the president of the Court. She tells him about Lord Asriel and his fortress and about Lyra and Will. He places her under arrest. Lord Roke reveals himself to Mrs. Coulter later that night, and the two become allies of a sort. In the middle of the night, a young priest comes into Mrs. Coulter’s room and steals her locket. Inside the locket is a curl of Lyra’s hair. Lord Roke follows the young priest and sees him give the hair to the president. The Consistorial Court is planning to destroy Lyra with a bomb made from her hair.
Lord Roke attempts to steal the hair back from the Consistorial Court, while Father MacPhail suspects that Mrs. Coulter has an accomplice. He brings her to a place called Saint-Jean-les-Eaux (Saint John of the Waters). In order to activate the bomb, they need to sever a human from its daemon and they intend to use Mrs. Coulter for this purpose. Mrs. Coulter and Lord Roke fight the troops and Mrs. Coulter escapes. Father MacPhail sacrifices himself, separating from his own daemon, who pleads with him not to cut them apart. The bomb goes off, despite Mrs. Coulter’s efforts to stop it. A witch in the service of the.Consistorial Court kills Lord Roke. Lord Asriel arrives in the Intention Craft and takes Mrs. Coulter away.
The ghosts of Lee Scoresby and John Parry find Lyra in the mass of ghosts and tell her that the Consistorial Court has made a bomb and that Lyra has to find the place were some of her hair was cut away and shave that spot. Will shaves it and puts the hair into another world. When the bomb explodes, it creates a vast abyss next to the path on which the children and the ghosts are walking. Lyra almost falls into the abyss, but a harpy rescues her. The ghost of John Parry tells Will and Lyra that their daemons have gone into Lord Asriel’s world, and that Will, Lyra, and the ghosts of Parry and Lee Scoresby have to go there.
Will and Lyra cut a hole from the world of the dead into a new world. Will and Lyra fall asleep in that world, and the dead come pouring out. When the ghosts hit the air, they dissolve. In the world of the mulefa, Father Gomez kills one of the tualapi, vicious swan-like birds, and tames the rest. In Lord Asriel’s world, Mrs. Coulter learns that Lyra is still alive, and that she and Will have freed the lost souls in the world of the dead. Lord Asriel and King Ogunwe discover that the Clouded Mountain, which is also called the Chariot, is approaching Lord Asriel’s fortress. Metatron is driving it. He intends to attack the newly founded Republic of Heaven that Asriel and his allies have built. Asriel calls all of his supporters to fight Metatron’s forces. Lord Asriel and his allies must protect Lyra and Will, who have been temporarily separated from their daemons. If Metatron gets to Lyra and Will first, he will be able to control them, using the knife to break their resistance.
Mrs. Coulter and Asriel talk. Mrs. Coulter discovers that Asriel wants to preserve Dust forever. In the world of the dead, some ghosts have hung back to fight the specters in Lord Asriel’s world. Lyra and Will lead them to an opening. Chevalier Tialys and Lady Salmakia are dying. Will opens a door into Lord Asriel’s world, where there is a battle raging, and the ghosts rush out to attack the specters. As the terrible battle rages, Will and Lyra realize that they can almost see the specters, and that they must find their daemons. They see Mrs. Coulter pass overhead in the Intention Craft and it appears she has escaped again to double-cross Lord Asriel. She enters the Clouded Mountain and meets with Metatron. She tries to seduce him in order to trick him. At the same time, a few angels are trying to escape unnoticed. They are carrying God out of the Clouded Mountain in a glass case. Lord Asriel, looking for Lyra, discovers the great abyss created when the bomb went off. Mrs. Coulter leads Metatron to the abyss, where she and Lord Asriel attack him. They drag him into the abyss, throwing themselves in with him to ensure that he doesn’t rise again. Back in Lord Asriel’s world, Lyra and Will find some cliff ghasts attacking God’s glass case. They kill the cliff ghasts and see that God is demented with age. They release God from the glass case, and he happily dissolves in the wind. Lady Salmakia and Chevalier Tialys die, and Madame Oxentiel leads the two children to Iorek Byrnison, who carries them closer to their daemons. They find the daemons but are attacked by specters. The ghosts of Lee Scoresby and John Parry save them. Lyra grabs Will’s daemon, Will grabs Pantalaimon, and they use the knife to escape into another world. The ghosts of John Parry and Lee Scoresby say goodbye to Will and Lyra and drift apart.
Lyra and Will fall asleep in the new world and wake to find that their daemons have gone again and they are in the world of the mulefa. Mary’s friends find them and bring them back to the village. Will and Lyra sleep again, and Mary goes to explore something the mulefa can’t explain. She finds the hole that Will and Lyra cut from the world of the dead and watches as the ghosts escape into the world of the mulefa. One of them turns to her before it dissolves and says, “Tell them stories.” Lyra goes down to the river to bathe without Will, feeling it would be strange to be naked in front of him. When Mary comes back, Will and Lyra befriend her. They discuss the many strange things that have happened and the things they have learned during their travels. Mary tells them she decided to stop being a nun because she met a man she liked who made her happy.
That night, Mary can’t sleep, so she goes to the grove of the seedpod trees. As she sits watching the sraf flow away, she realizes that she can see the clouds and the wind and the moon moving, trying to erect a barrier to keep the sraf from leaving the world. She realizes that the subtle knife was made 300 years ago, just the amount of time that sraf has been leaking out of the world through the holes made by the knife. As she is returning to the village, Mary sees Father Gomez approaching with the tualapi he has tamed. He goes into the village, but it he can’t find Will and Lyra and so he leaves. The next morning, Will and Lyra go to look for their daemons. Father Gomez is following them, but before he can shoot Lyra, Balthamos returns and snatches Father Gomez’s daemon. As Balthamos leads Father Gomez away from Will and Lyra, Lyra tells Will that she loves him. She feeds him a piece of fruit, and they kiss passionately. Balthamos kills Father Gomez and then dies himself, calling out for Baruch. That afternoon, Mary and Atal notice that the sraf is no longer flowing away. Instead, it is falling straight down, feeding the seedpod trees. Lyra and Will return hand in hand, and Mary sees that they are covered in sraf. It is their love that has stopped the sraf from flowing away. That night, Lyra and Will’s daemons meet Serafina Pekkala. Serafina names Will’s daemon Kirjava. She tells them that the daemons have to tell Will and Lyra something. Serafina then visits Mary and tells Mary that she, too, has a daemon, an alpine bird. The next day, Will and Lyra finally find their daemons. Kirjava and Pantalaimon tell Will and Lyra that the holes they made with the knife allowed Dust (sraf) to leak out of the universe, and that all of these holes need to be closed. Lyra and Will remember something that Will’s father told them: people have to live in their own worlds or they will get sick and die. Kirjava and Pan tell Will and Lyra that every time the knife is used, a specter is created.
Lyra tries to consult the alethiometer to see if the daemons are right that the knife creates specters and that every last hole has to be closed. She finds she can’t read the alethiometer. Will and Lyra realize that they have to leave each other and live in their own worlds. Xaphania appears and asks Will to teach her how to close the windows made by the subtle knife. She tells Will and Lyra that one window can be left open, but Will and Lyra know it has to be the window they opened for the dead. Xaphania tells them they have to break the knife. Xaphania leaves Will and Lyra to mourn their coming loss. Kirjava takes the form of a cat and Pantalaimon takes the form of a pine marten. Will puts his hand on Pantalaimon and Lyra puts her hand on Kirjava. They know their daemons won’t change shape any more. The next day, Serafina Pekkala and the Gyptians arrive in a boat to pick up Will, Lyra, and Mary. The mulefa show the Gyptians where the dead escaped and tell the Gyptians they are planning to plant a grove of seedpod trees around it, because it is a sacred place. Before Mary gets on the Gyptians’ ship, Atal and the other mulefa give her seedpod seeds and some of their precious oil. The Gyptians sail on until they pass into the world of Ci’gazze. Lyra decides to go with Will and Mary into their Oxford world one last time. Serafina Pekkala teaches Mary how to see her daemon. Lyra and Will go to Will’s Oxford together, and there they find a bench in a garden. The bench is also in Lyra’s world. They agree that, even though they must live in separate worlds, they will return to this bench every year and think of each other. Lyra returns to the world of Ci’gazze and Will closes the window behind her. Will breaks the knife by thinking of Lyra. Mary offers to help Will and his mother in their world. Three weeks later, Lyra is back at Jordan College. She tells the story of her adventures to the Master and to a female scholar named Dame Hannah, who offers to take Lyra under her wing and teach her. She promises to teach her how to use the alethiometer. Lyra accepts Dame Hannah’s offer. Lyra and Pantalaimon go to the bench in the garden. They talk about Will and Kirjava, and what their new life will be like, and what it will be like to have friends who are girls Lyra’s own age. Then agree they must find heaven whenever and wherever they are. The Amber Spyglass ends as Lyra and Pantalaimon resolve to establish a Republic of Heaven.