The Subtle Knife opens in a world very much like our own. A young boy named Will Parry is bringing his ill mother to stay with Mrs. Cooper, Will’s old piano teacher. Mrs. Cooper reluctantly agrees to take care of Mrs. Parry for a little while. Will returns to his house, where he lives alone with his mother. Men have been coming to the house looking for letters that Will’s father wrote to Will’s mother, and Will wants to find them before the men do. Just before Will finds the letters, the men arrive at the house. Will escape with the letters, accidentally killing one of the men along the way.

Will runs until he finds himself on a strange street. He sees a cat that reminds him of his own cat. The cat jumps through a window in the air, and Will follows her through and discovers that he is in a new world. The city he finds himself in seems to be deserted. Will seeks refuge in a small house, and there he meets Lyra. The pair are initially frightened of one other because Lyra has never seen anyone without a daemon and Will has never seen a daemon.

Elsewhere, Serafina Pekkala sees Mrs. Coulter torturing a witch to find out what the witch knows about Lyra. Serafina kills the ailing witch to prevent her from telling Mrs. Coulter what she knows. Serafina goes to Svalbard, where she meets Lord Asriel’s servant, who tells her that Lord Asriel means to start a war with God. Serafina flies back to her clan and to Lee Scoresby. Ruta Skadi, the queen of the Latvian witches, has joined them.

Lee Scoresby says that he is going to look for a scientist and explorer named Stanislaus Grumman. Serafina and her witches decide that they need to summon other witch clans to fight on Lord Asriel’s side and protect Lyra. Ruta Skadi will go to Lord Asriel to see what he is really doing.

Back in the new world, Lyra and Will meet two children named Angelica and Paolo. They tell Will and Lyra that the city they are in is called Cittàgazze (or Ci’gazze), and that it is filled with specters, which are wraiths that feed on adults. Specters cannot harm children and children cannot see specters.

Lyra and Will agree to go to Will’s Oxford. Lyra wants to find a physicist who can tell her about Dust and Will wants to find out more about his father, an Arctic explorer who disappeared before Will was born. Will’s mother always said that Will would take up his father’s mantle.

Lyra goes first to a museum where she meets an old man who seems very interested in her. While examining skulls in a case, Lyra learns from the alethiometer that the skulls of people who lived more than 33,000 years ago have less Dust around them than the skulls of people who lived more recently. After consulting the alethiometer, Lyra finds a physicist who can help her. This physicist is a former nun named Mary Malone who researches dark matter and something she calls Shadows. Mary explains that Shadows are conscious and they cluster around humans—they are the same thing Lyra calls Dust. Lyra convinces Mary that she can talk to Shadows. Will learns more about the Arctic expedition his father was on just before he vanished. Back in Ci’gazze, Will reads his father’s letters and finds out that just before he disappeared, his father was looking for the same kind of hole into another universe that Will fell through. In Lyra’s world, Lee accidentally kills an agent of the Church. Serafina and her witches enter the world of Ci’gazze and learn about the Specters. Ruta leaves the witches to follow a flight of angels to Lord Asriel’s fortress.

Though Lyra and Will are the same age and are from the same city (albeit the same city in different worlds), they couldn’t be more different. Lyra is an independent, irreverent scamp, whereas Will is somber and responsible. Lyra’s adventures have been fantastical affairs involving daemons, talking bears, and witches. Will, on the other hand, must deal with painfully real problems, looking after his ailing mother and protecting her from real and imagined foes. What Will and Lyra do have in common is a lack of strong parental figures. Lyra’s mother and father have been hidden from her for most of her life and she has never lived under strict supervision. Will’s father is missing and his mother relies on him for structure and support. Because both Will and Lyra have largely raised themselves, they are free to set out on adventures.

In Ci’gazze Will and Lyra meet the fierce Angelica and her stupid little brother Paolo, who tell them about specters, which are unique to their current world. Like Dust, specters point to a fundamental difference between adults and children. They feed on the life force and energy of adults. Children, who are still in the process of being formed, can’t even see specters. Specters can sense when a child’s soul is starting to take its final formation and they hover around these children.

Also in this section of the book, Lyra meets Dr. Mary Malone, who studies dark matter. Scientists in our own world have long been intrigued by dark matter. The existence of dark matter was posited when people realized that even with all the known planets and suns, gravity should make the universe collapse in on itself. This logical problem led to the idea that matter that is undetectable—dark matter—exists. Dr. Malone and her colleague Oliver Payne have been trying to prove this theory. Not only do they believe that dark matter exists but they also think that it has consciousness. They try to communicate with Dust through computers. They refer to dark matter as “Shadows.” When Lyra appears and is able to communicate with their computer using the skills she has learned through the alethiometer, she proves that dark matter is conscious and does respond to human thought. Together, Lyra and Mary discover that dark matter, Shadows, and Dust are the same thing.

Lyra’s discovery that the reduced Dust levels around the skulls of people who lived more than 33,000 years ago suggests that humans were not always conscious, spiritual beings. Since Dust is only attracted to full-fledged humans, the lack of dust around certain skulls tells us that before 33,000 years ago, humans were more like other animals than they are today. They were alive, but they did not have the ability to make decisions or live deliberately.

Just after Lyra’s discovery, Will learns that his father was looking for windows into other worlds just like the one that Will went through to get to Ci’gazze. This means that the windows are not a new phenomenon. They have been around at least as long as Will has been alive. It also means that perhaps Will’s father is not dead. It is possible that he wandered into another world and got lost or has been unable to return.

As in Milton’s Paradise Lost, in which a group of angels follows Satan, a war party of angels goes to join Pullman’s Satan figure, Lord Asriel. What Ruta Skadi learns about the angels during her flight with them is almost as interesting as what she learns from them. The angels are ancient, sexless beings. They are shaped like humans, but unlike humans, they wear no clothes. Unlike Adam and Eve, who felt ashamed of their nakedness after eating from the tree of knowledge, the angels don’t know shame. But this also means that they are not as aware of their physical beings as humans are. In Pullman’s fictional universe, angels envy humans their short lives because humans have bodies and can experience desire and pleasure and pain.

In the world of Ci’gazze, Lyra awakes before Will. She goes to Will’s Oxford without him and visits Mary Malone. Some officials from Will’s world are already there in search of Will, and Lyra accidentally reveals that she knows him. Lyra flees and is picked up by the man she met in the museum the day before. His name is Sir Charles Latrom, and he takes Lyra to the window that leads to Ci’gazze. Before he drops her off, Sir Charles steals her alethiometer.

Lyra returns to Ci’gazze to tell Will what happened. She is devastated. That morning, the alethiometer had told her to help Will find his father, and instead she went off on her own mission. She vows that as soon as they get the alethiometer back, she will devote herself to helping Will.

Together Lyra and Will go to Sir Charles’s house, where Sir Charles tells them that he will give back the alethiometer if they get him a knife that is being held by a man in Ci’gazze, in the Torre degli Angeli (Tower of the Angels). Lyra and Will go to the Torre and see Angelica’s older brother Tullio trying to use the knife. Tullio has ambushed and beaten an old man named Giacomo Paradisi and stolen the knife from him. Tullio wants to use the knife to defeat the specters and to travel between worlds. Will and Tullio fight for the knife. Tullio cuts off two of Will’s fingers but Will wins the fight and keeps the knife. Tullio escapes. Giacomo explains that a knife bearer is known by his absence of two fingers. He also explains that the knife was made 300 years ago and that the scholars from the Torre degli Angeli have been using it to cut into other worlds ever since then.

Giacomo teaches Will both how to cut through to other worlds and how to close up the holes again. Specters attack Tullio and eat his soul. Later that night, Lyra and Will return to Will’s world, planning to use the knife to steal the alethiometer. While they’re at Sir Charles Latrom’s house, Mrs. Coulter arrives. Lyra realizes that Sir Charles Latrom is actually Lord Boreal, a man from her own world, not Will’s. Like Tullio, Lord Boreal wants the knife so he can travel between worlds without fearing the specters.

When Will takes Lyra to confront Sir Charles Latrom, he sees that Sir Charles has a small snake—his daemon—in his sleeve. Will barely manages to get the alethiometer. Mrs. Coulter’s monkey daemon chases them, but Will and Lyra escape.

Back in Lyra’s world, Lee Scoresby finally finds Stanislaus Grumman, who is now a shaman in a group of Tartars. Lee discovers that Grumman’s real name is John Parry and that he is Will’s father. Parry is now trying to find the knife bearer so that he can tell him something important. Lee agrees to take John to the world of Ci’gazze in his balloon. Back in Ci’gazze, Will and Lyra are attacked by a group of angry children and are almost killed, but Serafina Pekkala and her clan rescue them and bring them away from the city. Serafina notices that Specters seem to be afraid of Will’s knife.

In Will’s world, Mary Malone figures out a way to talk to the Shadows through the use of her computer. The Shadows tell her to go into Ci’gazze. Mary’s fate is somehow connected with that of Will and Lyra and she realizes that she has to play the role of the serpent by bringing about a new fall from grace. Mary leaves her world and enters Ci’gazze. The witches attempt to heal the wound Will incurred during his fight with Tullio, but their spell doesn’t work. While she is trying to cure the wound on Will’s hand, Serafina says that she is afraid of Will because he is so fierce.

Lyra, Will, and the witches travel north toward the rent in the sky that Lord Asriel created. Ruta Skadi returns to Serafina’s clan and reports that Lord Asriel has built a magnificent fortress in another world, and creatures from every world have joined him in his war against God. Ruta overheard cliff ghasts say that something called Æsahættr is the only thing that could destroy God. After the children go to sleep, Serafina discovers that angels have come on a pilgrimage to see Lyra.

In this section, Will and Lyra realize that the man who calls himself Sir Charles Latrom is originally from Lyra’s world, where he is known as Lord Boreal. The fact that Sir Charles is a wealthy, important man in Will’s world implies that he has been traveling back and forth between the two worlds for many years. It also suggests that perhaps there are many people who live in more than one world.

Lyra first met Lord Boreal at the party at Mrs. Coulter’s house, which is why he recognized her in the museum and knew she had the alethiometer. Lord Boreal is one of the people in charge of the General Oblation Board. Some people on the Board participate out of religious interest, but Lord Boreal seems more interested in power and in winning Mrs. Coulter’s affections. He knows about Ci’gazze and knows that he needs the knife to survive there.

Will’s battle with Tullio for the knife is not as important as the knife itself. We learn that ever since its creation 300 years ago, the knife has been used to cut though to other worlds. We also learn that the knife is somehow connected to the specters. The man that Serafina Pekkala encounters while she is looking for Lyra and Will mentions that the world of Ci’gazze was once a prosperous and peaceful world and that specters didn’t exist until about 300 years ago—exactly when the knife was created. Specters are afraid of the knife: both Tullio and Sir Charles Latrom wanted the knife so that they could travel in the world of Ci’gazze and not be harassed by the specters.

Lyra realizes that she got both herself and Will into trouble by ignoring the alethiometer’s instructions to help Will find his father, and she decides to devote herself to Will’s cause when she gets her hands on the alethiometer again. The witches, because they have come to help Lyra, also have to help Will. The alethiometer is what leads them north.

When Serafina Pekkala meets Will, she notices his unusual fierceness and gravity. Lyra is lovably impulsive and wild and openhearted, but Will is dignified and almost adult in his composure. Throughout the trilogy, many people remark that Will’s single-mindedness and sense of purpose make him almost fearsome. Still, in many ways Will is just a boy looking for his father.

Biblical and Miltonian themes run through this section. When Mary figures out how to talk to the shadows, they tell her that she has to “play the serpent” for Will and Lyra. This is a reference to the Book of Genesis, in which a serpent tempts Eve to eat from the tree of knowledge. It is also a reference to Milton, whose version of the story depicts the serpent as Satan in disguise.

Ruta Skadi’s reports of Lord Asriel’s fortress echo Milton’s description of Satan’s rebellious army of angels. The angels’ pilgrimage also recalls biblical stories of people making pilgrimages to see holy events. The fact that angels travel from afar to keep a momentary vigil over Lyra suggests that Lyra is a figure of the highest importance.

Lee Scoresby and John Parry are sailing in the skies of the world of Ci’gazze, with forces from the Church in hot pursuit. The Church’s agents, who travel in zeppelins, gain on Lee’s balloon. Lee has to make a crash landing and abandon the balloon. Parry uses magic to bring down three of the four zeppelins that are pursuing them. Lee agrees to keep the soldiers in the fourth zeppelin at bay while Parry escapes to find the knife bearer. Lee holds the soldiers off with the help of his daemon, Hester, and Parry escapes, but Lee and Hester are killed. Before they die, they call out to Serafina Pekkala for help. Serafina leaves Will and Lyra in the care of her witches and goes to find Lee. Will explains that he knows he has to find his father because his mother always told him that he would take up his father’s mantle. One of the witches, Lena Feldt, sees people in the distance and goes to investigate.

Lena arrives at a camp and finds Mrs. Coulter and Lord Boreal. Mrs. Coulter, who has learned how to control the specters, uses one to capture Lena Feldt’s daemon and torture Lena. Mrs. Coulter forces Lena to tell her what she knows about Lyra. Lena says that Lyra is the new Eve and that she will cause a new fall from grace. Mrs. Coulter decides she has to kill Lyra rather than allow the second Fall. She kills Lena and Lord Boreal and summons the specters.

Up the mountain, Will can’t sleep, so he goes for a walk. In the darkness, Will runs into a man. Will and the man fight, and the man realizes that Will is the knife bearer. The man is John Parry. He cures Will’s wound and says that Will has to bring the knife to Lord Asriel. The knife, he says, is the one weapon that can kill God. Will tries to give the knife to Parry, but he refuses it, saying that the knife belongs to Will. He says it is in Will’s nature to be a fighter, and Will can’t deny his own nature. Parry lights a lamp so he can see Will. Just as Will realizes that he is looking at his father, a witch who had been in love with Parry kills him and then herself. Will takes his father’s cloak and leaves to find Lyra.

As Will heads toward the camp, he meets two angels who urge him to go with them to Lord Asriel. They were watching over Parry to make sure that he gave Will his message. Will says that before he does anything he has to go back to Lyra. When he returns to the camp, Will sees that Mrs. Coulter and her army of specters have already attacked. The witches are all dead and Lyra is gone. She has left her alethiometer behind. The angels try to get Will to forget Lyra and come with them to Lord Asriel. They want Will to bring the subtle knife so that Will and Lord Asriel can use it against God. Will stares at Lyra’s knapsack, which contains the alethiometer, unable to decide what to do.

There are benefits to having a daemon, but there are also some obvious downsides. Because daemons are the physical incarnation of a person’s soul, their existence means that people’s souls are vulnerable to attack. This means, for example, that even though Lena Feldt is well hidden, her inattentive daemon leaves her vulnerable to Mrs. Coulter’s spectral forces. Touching another person’s daemon is a great taboo in Lyra’s world, precisely because the daemons are so vulnerable. In The Golden Compass, Lyra experiences an appalling shock when a man in Bolvanger grabs Pantalaimon.

Relations with one’s daemon vary depending on the person in question. For example, like the witches and their daemons, John Parry can exist far apart from his daemon, Sayan Kötör. Characters like these, who possess some sort of magic or extraordinary power, are able survive far away from their own souls.

In this part of the novel, Lena Feldt tells Mrs. Coulter that Lyra is the new Eve. As in the Book of Genesis and in Paradise Lost, Eve will cause humanity to fall again. Mrs. Coulter, who is power-mad and on the side of the Church, will do whatever she can to stop Lyra from fulfilling this destiny. But in Pullman’s fictional world, a second Fall is actually a desirable outcome. The Church calls the result of the first Fall sin, but Pullman considers the result consciousness and choice. Pullman portrays the first Fall as the beginning of knowledge and true humanity. A new Fall would not mean not sin and darkness, but freedom from the repressive Church.

John Parry’s insistence that Will not deny his nature sounds like an argument that destiny does exist and Will has no choice but to fight. This seems at odds with Pullman’s enthusiasm for choice and free will, as does the fact that several characters consider Lyra fated to be the new Eve. This apparent contradiction is left unexplained at this time.

We also know, from Will’s brief and painful conversation with his father and from the angels’ insistence that Lord Asriel needs Will’s knife, that the subtle knife is probably the Æsahættr that Ruta Skadi overheard the cliff ghasts talking about. It is not just useful for getting between worlds and for keeping specters away. It is the one thing that can kill God, which is why the rebel angels want it so badly. John also tells Will that the two sides now aligning for battle have been fighting since humanity came into existence. God’s side demands submission and obedience from its opponents, while Satan’s side wants to increase the knowledge and enlightenment of human beings.

The witch who kills John Parry and herself is, to Will, inexplicable. The passion and fury that love has inspired in her don’t make sense to him. Love doesn’t strike him as something worth killing and dying for. Despite his growing friendship with Lyra, Will has not yet left his childhood innocence behind, and he has no real understanding of sexual passion.

Will’s mother said that one day Will would take up his father’s mantle. After his father dies, Will literally takes up his mantle (mantle is another word for cloak). In a symbolic sense, Will takes up his father’s mantle as a fighter.