Will grew up knowing that he needed to find his father. His mother had always done some strange things such as thinking that people were after her, but as it turns out, she is right. Some men keep coming to the house pestering her about some letters his father, the explorer, had written to her. Before he sets off on his journey, he leaves her with his old piano teacher. He goes home to rest before setting out. Will wakes up to people in his house. He grabs the green case that holds the letters they are after, but isn't quick enough to get out in time. He rushes one of the men to surprise him, but the man trips over the cat, Moxy, falls down the stairs, and dies. Will rushes out of the house heading towards Oxford. While trying to keep inconspicuous, a stray cat leads him to a window to another world. The world seems empty and as he's about to go into a building, he is attacked by Lyra, who is also confused about him. She finds it very odd that Will doesn't have a demon. He finds Lyra's lack of worldly knowledge frustrating.
Meanwhile, Serafina Pekkala spies on the zeppelin that holds Ms. Coulter, seeing the evil woman and her monkey trying to torture information out of another witch. Serafina kills the other witch before she can give too much away and vows to kill Ms. Coulter. She meets up with Lee Scoresby and invites him to join her at the meeting the witches will be having. At the meeting, Lee gives his opinion on what is going on and informs the witches that he is going to search for Stanislaus Grumman to find information on the object that will protect its holder. Serafina gives him a flower for him to use to call her should he ever need her help. A witch from a different clan, Ruta Skadi (who also used to be Lord Asriel's lover), tells the witches of the atrocities going on in the south in the name of the authority. The witches set off on a search for Lyra.
Lyra and Will meet some other kids that tell them about the spectres, strange creatures that only attack adults. They eventually decide to go back to Will's world so that they can each perform certain tasks. Will goes to the library to inquire about his father's last known expedition. Lyra meets a strange man at a museum, but wonders on to find a scholar that is studying Dust (dark matter), Mary Malone. Lyra suggests to her that she get her machine to use words to answer her questions like the alethiometer does with pictures for her. Will and Lyra meet up and return to the other world, Cittàgazze, they find the children throwing rocks at a cat and Will, Lyra, and Pan save it.
Lee Scoresby is up north and finds an observatory. He goes in to question the inhabitants about Stanislaus Grumman. However, he takes the conversation a little far by asking about Dust and ends up having to kill them all to save his life. He takes the ring of the one that was working for the magistiruim. He eventually finds Stanislaus Grumman and they head off in the balloon to find the bearer of the Subtle Knife.
While Will is sleeping, Lyra goes back to his world to see how Dr. Malone is progressing. However, when she arrives at the lab, she is questioned by policemen. They mention Will to her and she runs away from the, barely escaping. The stranger from the museum gives her a ride close to the window to Cittàgazze and she goes back to Will only to find that the man, Sir Charles Latrom, (who is actually Lord Carlo Boreal from her own world) has stolen her alethiometer. Her and Will set off to retrieve it from him, and he makes them a deal. He will give her the alethiometer if they bring him the Subtle Knife. They go back to Cittàgazze and in the tower is a man wielding the knife against what must be spectres. In the process of getting the knife from Tito, they children meet the old bearer of the knife. He tells will that he must know bear the knife because he lost his last two fingers on his left hand, same as the old bearer. He teaches will how to work the knife to open windows and clothes them. Lyra and Will head back to Sir Latrom's and steal back the alethiometer. They escape to Cittàgazze to find the other children in a murderous rage because they killed the older sibling of two of them. The witches come along and save them, explaining that they are acting as Lyra's guardians. They set off in search of Will's father. Will is still bleeding from the stumps where his fingers used to be.
Mrs. Coulter and Sir Latrom discuss over wine what the Subtle Knife is. As soon as she has the information she needs, she poisons him and finds that a witch has been spying on her. She tortures the witch into telling her that Lyra is Eve. Mrs. Coulter sets off to find Lyra to prevent her from making the same mistake that Eve did.
Lee and Stanislaus cross over into Cittàgazze, heading towards Lyra and Will, but they are being followed by another balloon. When Lee sees that there are also four zeppelins, they decide to land in the trees and hide. Throughout the night, Stanislaus is able to take down three of the zeppelins using his shaman magic. As Lee and Stanislaus are running, the last zeppelin spots them. Lee fights them off so that Stanislaus can escape.
Will wakes up to be confronted by Stanislaus, who he tries to fight away. Eventually, Will realizes that Stanislaus is there to help him. Stanislaus puts a salve on his stumps and they stop bleeding. He then tells Will that he must help Lord Asriel. He lights a match and he and Will both realize who the other was. Just then, the witch who Stanislaus had refused the love of shoots him through the heart. Will is furious with her, but lets her live. She drives a knife into her own heart. Two Angels show up telling will that it is time for him to help Lord Asriel, but he ignores them to check on Lyra. He gets back to the cave where they were sleeping to find her gone. He rucksack containing the alethiometer left behind.
His Dark Materials:
The Golden Compass
The Subtle Knife
The Amer Spyglass