Lyra spends the next few days trying to plan how she can stow away and join the expedition. She dismisses most of her plans. When she's not plotting, she pesters the men in charge. She's most eager to help Benjamin de Ruyter, the man in charge of spying, but when he disappears Lyra turns her attentions to Farder Coram. Farder Coram indulges Lyra and listens to her talk. Lyra is especially taken with Sophonax, Farder Coram's large, tawny cat dæmon. Her fur looks luxurious, but because touching another person's dæmon is taboo, Lyra only dreams of touching her. While Sophonax is sleek and healthy, Farder Coram walks tremblingly on two canes. His mind is as sharp as anyone's.
Sophonax's beautiful and healthy appearance indicates that whatever is going on with Farder Coram's body, his mind is still that of a young man's. This offers the reader another way to judge a character based on their dæmon and its characteristics. Importantly, Farder Coram treats Lyra with the respect that the other adults aren't at this point. This will mean that Lyra is more willing to trust him and let him in on her thoughts, which opens her up to his mentorship and helps her learn how to behave as an adult.
Lyra begins to ask Farder Coram for help interpreting the symbols on the alethiometer. She explains how she asked the alethiometer a question about how Benjamin de Ruyter's mission is going. The needle stopped on a symbol that can mean death, but they wonder if Lyra is interpreting it correctly. A man knocks and asks Farder Coram to come quickly: Jacob Huismans, who was with Benjamin, returned and is seriously injured. Lyra follows Farder Coram to a boat. Jacob Huismans is sweaty with pain, but tells Farder Coram that Benjamin is dead. He explains that they broke into the Ministry of Theology. His dæmon takes up the tale and says that they captured three Gobblers, who suggested they find out more about the Ministry and Lord Boreal.
Jacob Huismans's story shows Lyra and Farder Coram that the alethiometer isn't something to mess with. It can and will tell the truth; it's up to the humans reading it to correctly interpret what it says. For Lyra in particular, this starts to teach her that she needs to trust the alethiometer to lead her in the right direction. Importantly, this both leads Lyra toward her destiny in the North and toward a more mature understanding of the world around her.
The dæmon says that their opponents seemed to know everything they were going to do. They all went to a side door and were ambushed in the dark once inside. The physician arrives, so Farder Coram pulls Lyra away. He tells her to occupy herself until later, when they need to talk about the alethiometer. She and Pan sit on a bank and Lyra thinks that she's afraid of her ability to read the alethiometer. They discuss that it might be a spirit that moves the needle, but Pan thinks it's elementary particles. Lyra recalls a holy object at Gabriel College, which has sails that spin when the light—and elementary particles—hit it. Tony interrupts Lyra and sends her to find John Faa and Farder Coram at the Zaal. John Faa says that Jacob Huismans has just died—and they need to take Lyra with them to the North.
The intersection of physical science and religion makes religion easier to see at work in the real world—and also means that controlling society through religion and the related sciences is even easier for the Magisterium. Rather than existing in writing, ritual, and the minds of believers, in Lyra's world, religion is something testable and observable to the masses in concrete ways that don't rely solely on having faith.
The next two weeks are difficult for Lyra. They're busy, but she has to remain hidden and being inside all the time is difficult. Tony Costa tells her about strange rumors that she escaped from the Gobblers, or that she and Pan are spirits or spies for the Tartars. Lyra longs to be free, and sometimes wishes she were back at Jordan College with Roger. She spends much of her time studying the alethiometer and finds that if she concentrates, she can read and interpret it. She tells Farder Coram that she just innately understands what the alethiometer is telling her. One day, he asks her to find out what Mrs. Coulter is doing. The long needle swings around and stops several times at a picture of a lizard-like creature that Lyra doesn't recognize.
The desire to return to Jordan College and have things be the way they once were is a perfectly normal desire for Lyra—and would be even if she hadn't been thrown into a journey like this. This reminds the reader that in many ways, Lyra is just a normal child going through the normal changes that all children do as they move toward adulthood—although in circumstances that are far from normal. Like all children, there are gaps in her knowledge, which can at times lead to disastrous consequences (as this gap will).
Lyra asks if she can go outside for a minute. Farder Coram decides that it won't hurt, so Lyra and Pan leap up. Pan turns into a seagull and plays in the wind and the water. Lyra shares in his joy even though she's cold. Suddenly, something small and black attacks Pan. A second attacker joins the first. The tillerman's cormorant dæmon rescues Pan, who falls into Lyra's arms, turns into a wildcat, and leaps on the fallen creature that attacked him. The second attacker escapes. Lyra puts a tin mug over the creature and she and Farder Coram take it below.
Being attacked like this reminds Lyra that she's both wanted and vulnerable, given her connections and the fact that she's a child. When Lyra shares how Pan is feeling as he plays, it suggests that a person needs fresh air and moments like this in order to feel whole and at peace—but also that these innocent moments can be the most dangerous.
Farder Coram dumps the creature into a glass. It looks like a large and furious beetle. Farder Coram explains that it's not a live creature: it's a bad spirit trapped in a clockwork body. He says they come from Morocco, and this one was certainly sent by Mrs. Coulter. Lyra realizes that the lizard symbol means air, and Farder Coram says the symbol is a chameleon, which lives on air. Lyra and Farder Coram stare at each other in awe, and Lyra says they should've listened to the alethiometer. They decide to shut the "spy-fly" in a tin.
Just as with Jacob Huismans, the spy-fly impresses upon Lyra and Farder Coram that they can and should rely on the alethiometer to tell them what to do and what's going to happen—and importantly, that they can't ignore something just because Lyra can't figure it out. However, learning that the chameleon can denote air will, going forward, allow Lyra to interpret the alethiometer better.
The boat reaches Colby and Lyra accompanies Farder Coram and the tillerman through the empty town to the docks. There they find Tony Costa, who quietly says that a gyptian man was killed. The ship to go north is huge. They climb up the gangway and head below to find John Faa and tell him about the flying spirit. He doesn't reprimand them for letting Lyra outside. Being the only female on the ship, Lyra gets her own cabin. Once she stows her things, she excitedly looks out the window to watch England disappear. She can't see through the heavy mist and soon, both she and Pan are seasick.
The dead gyptian again reinforces that the gyptians are in a vulnerable state because of the way that other people perceive them. Going north to rescue children and, in effect, going against the Magisterium means that they're becoming even more vulnerable. However, they are fighting for others and, morally speaking, are doing the right thing—their targeted identity just makes their mission harder to carry out.