The Angels, Baruch and Balthamos, explain that they need to present Will to Lord Asriel so that he will believe the information they have to give him. Will refuses, realizing that since these creatures don't have physical bodies, he is stronger than them. He is determined to find Lyra. The angels fly around looking. Balthamos returns to Will and they start walking down the mountain. The find the spot where Mrs. Coulter kill Sir Charles. Will scavenges for supplies and figures out how to use the knife more consistently. When the other angel returns, they make it quite obvious that they are lovers. Will sends Baruch to Lord Asriel, while Balthamos is to help him find Lyra. Baruch is attacked on his way to Lord Asriel and dies shortly after delivering the message to him. Balthamos is overwhelmed with grief over the death of his lover.
Serafina travels to Svalbard to inform Iorek of Lee Scoresby's death, and how she has placed a spell on it so that the body will not decompose until Iorek has had a chance to see him. The bear travels to the other world and eats the body of his friend, swearing revenge before returning to his own world to lead his bears south where the climate is still cold.
Mrs. Coulter is living in a cave, keeping Lyra asleep. There is a little girl, Ama, that is fascinated by Lyra, and wants to help. She brings Mrs. Coulter supplies and eventually goes to see the medicine man. She lies to the man so that he won't be suspicious of the sleeping girl. Upon returning to the cave, the girl plans to give Mrs. Coulter the remedy, however, she decides to hide from Mrs. Coulter and sees her abuse Lyra in her few waking moments. Lyra keeps dreaming of Roger in the World of the Dead. She promises that she will come for him.
Department of Discipline sends an assassin, Father Gomez, for Lyra before she can be tempted by Mary Malone.
Mary Malone is wondering through worlds. she uses the Chinese signs to guide her to where she should be. The spectres of Cittàgazze are afraid of her, so everyone wants her to stay with them to keep themselves safe. Mary keeps moving through worlds until she finds the Mulefa (invertebrates with a diamond-shaped skeleton, and claws that they hook into seedpods for mobility)
In Will's travels, with Balthamos disguised as his deamon, he comes across a city that is being terrorized by the armored bears. Will challenges Iorek, who accepts. Will asks for a piece of Iorek's armor to even his chances, Iorek accepts. Will uses the knife to cut up the helmet with ease. Iorek realizes that he will not be able to beat the child as long as he has the knife. The people finally agree to refuel the bears' boat and Will travels south with them.
Upon arriving in the south mountains where Baruch told Will and Balthamos they could find Lyra, Iorek orders the bears away until he calls for them again. Will, Balthamos, and Iorek start their search for Lyra. They meet the village girl that has been helping Mrs. Coulter and she helps them with a plan to get Lyra back. However, their time is limited as the Magistirium and Lord Asriel have both sent forces to kill/save Lyra, respectively. Will decides to talk to Mrs. Coulter first, which is a mistake as she successfully uses her charm on him. He goes back while she is sleeping, making a window from another world into the cave. However, before he can make a new window to escape, Mrs. Coulter wakes, reminding Will of his own mother. His concentration is split and the knife breaks into several pieces. The Gallivespian spies, the Chevalier Tialys and the Lady Salmakia (tiny people about the size of a hand, whose life spans are about 10 years) sting Mrs. Coulter with their spurs. Will gets away with Lyra. However, Balthamos is frightened of the war and still struck with grief and flees as soon as the danger starts. Iorek, with regret, fixes the knife for Will, before he returns north to Svalbard.
After Lyra is waken up, the Gallivespians want to take the children to Lord Asriel. The children refuse, as they know they have a different mission to complete. They start their trek to the World of the dead with the Gallivespians reluctantly following.
Lord Asriel's alley, King Ogunwe, takes Mrs. Coulter after the fighting in the mountains is over. Lord Asriel, having a soft spot still for Mrs. Coulter, allows her to learn all about his forces. After she has heard enough, she steals his intuition-craft and returns to the Magistirium, where she is imprisoned. Lord Roke, the Gallivespian leader, tags along and finds that the Magistirium has a bomb that will kill Lyra using a lock of hair they found in Mrs. Coulter's locket. Mrs. Coulter and Lord Roke attempt to prevent the explosion, but are unable to, resulting in Lord Roke's death.
Will, Lyra, and the Gallivespians have to take a boat ride to reach the World of the Dead. However, the boatman informs Lyra that she must leave her deamon, Pan, behind. The others also feel the loss of their deamons as the boat starts making its way across the river. Upon reaching the other side, they meet the Banshees. They ask for a story and Lyra begins to spin her web of lies. However, they know that she is lying and yell at her. Eventually, she finds Roger and they decide to find a way to lead the spirits out of the grey nothingness of that world. The Banshees agree to help them find the way if the dead will tell them the true stories of their lives.
Mary Malone continues to live with the Mulefa, learning the ways of their society. They teach her that Dust is actually self-awareness. Realizing that she cannot see Dust like they can, one Mulefa teaches her how to see it using two pieces of glass. Eventually, she makes this into the amber spyglass. She repays the Mulefa for the hospitality by helping them find out with the trees with the seedpods that they need to survive are dying. She eventually finds that the trees are not getting enough Dust to reproduce.
While making their way through the underworld, Will and Lyra meet Lee Scoresby and John Parry, who commit themselves to helping as much as possible. They start by having Will cut the strand of hair that they were going to use to operate the bomb. Will takes the hair and puts it into the wall of another world, where it explodes. John Parry informs them that they cannot live in other worlds for very long without becoming ill and eventually dying early. They open a doorway into the Mulefa's world and allow the ghosts to be free. The spirits dissolve into Dust as soon as they leave the underworld. With their mission complete, they go to the world where Lord Asriel's army resides to find their deamons.
On their way to Lord Asriel's fortress, they see the Authority in a crystal prison being attacked by cliff-ghasts. The fend off them off and release him from Metatron's cage, but the Authority still dies from weakness. The children continue the search for the deamons with Will's father, John Parry, leading the way. The Chevalier Tialys and the Lady Salmakia die along the way. Will grabs Pan and Lyra grabs Will's deamon, and they escape to another world. Meanwhile, Lord Asriel and Mrs. Coulter have sacrificed themselves to take Metatron down into the abyss to save Lyra.
Will and Lyra wake up in the world of the Mulefa, finding themselves once again without their deamons, but thankfully without the pain of being separated. The Mulefa find them and take them to Mary. They tell her their entire stories and she talks about love. They go to search for their deamons while Mary observes that the Dust is going wild and destroying the trees. Father Gomez lines up a shot to kill Lyra, but Balthamos distracts him. He leads the assassin up the river away from the children that are busy falling in love. Father Gomez learns how to see Balthamos, but is still killed by him just before the angel dies himself.
The children pledge their undying love and "lie together" under the trees by the river. At this moment, the Dust settles, allowing the trees to germinate once again. Because of what John Parry told them, they know that they must go to their own worlds, but decide that Will can use the knife to visit. Lyra goes to check the alethiometer to see if they are making the right decision, but is unable to read it anymore. However, they learn from their Deamons that Dust is escaping through the windows that the knife has made. All of the windows must be closed. The angel that appears to explain this all to them will allow one window to be left open, but they decide that it should be the one from the World of the dead to the Mulefa's world. They decide that they must destroy the knife because every time a window is made, so is a spectre. And so, the young lovers must be separated to live long full lives where they can be useful members of society, telling what they have learned. Will and Lyra decide to have a special place that exists in their respective Oxfords where they will both go once a year, never forgetting their love.
Lyra decides to devote her life learning how to read the alethiometer.
His Dark Materials:
The Golden Compass
The Subtle Knife
The Amer Spyglass