Two years after the conclusion of The Amber Spyglass, Lyra and her daemon Pantalaimon sit high on the roof of Jordan College, gazing down on the streets of Oxford. But their peace is shattered by a flock of enraged starlings, who seem intent on knocking another bird out of the sky – a bird that Lyra and Pan quickly realise is a witch’s daemon. The daemon carries worrying tidings of a terrible sickness spreading in the north, and claims that only Lyra can help him – but is he really friend, or foe?

When Lyra is studying at Oxford University, she comes across the story of Lee Scoresby and Iorek Byrnisson's first meeting, many years ago, along with much evidence of the adventure that brought them together. When a young Texan balloonist, Lee Scoresby, comes down to earth in the harbour of an Arctic town in the North, little does he realise that he is about to be embroiled in an out-and-out political brawl.

Lyra is now studying at St Sophia's College, Oxford, with her daemon Pantalaimon. But, for the first time there are serious divisions between the two. Lyra is questioning everything she once held dear. Pan misses the impulsiveness of their youth. When an act of terrible violence breaks the peace of the Oxford night, Lyra and Pan's relationship reaches a crisis and they are drawn, far from home, into the dangerous factions of a world they had no idea existed.

Malcolm Polstead's Oxford life has been one of routine, ordinary even. He is happiest playing with his daemon, Asta, in their canoe, La Belle Sauvage. But now as the rain builds, the world around Malcolm and Asta it seems is set to become increasingly far from ordinary. Finding himself linked to a baby by the name of Lyra Belacqua, Malcolm is forced to undertake the challenge of his life and to make a dangerous journey that will change him and Lyra for ever.