While under Mrs. Coulter's guidance, Lyra learns of her mentor's critical role in Church's General Oblation Board, a.k.a. the Gobblers, the party responsible for the disappearing children. It is revealed that these kidnapped children are taken to Bolvangar, a place in the far North, to participate in Dust experiments whereby they are severed from their dæmons through a process called intercision. Lyra also learns that the Church has captured and imprisoned Lord Asriel in the Arctic region of Bolvanger where he has undertaken Dust experiments of his own.

Horrified at what she has learned, Lyra and Pantalaimon flee Mrs. Coulter's home in the middle of the night and are rescued through the kindness of two gyptian men. The gyptians are a gypsy group of boat-people who live a harsh life on the water tempered by their unwavering sense of family, loyalty and love. It is the gyptians' children who have suffered most at the hands of the Gobblers, and they have vowed to travel North to rescue them. Lyra pledges to share what she knows, rescue her dear friend Roger, and ultimately find her imprisoned father. Through the gyptian elders, Lord Faa and Farder Coram, Lyra is bewildered to learn that her parents are Lord Asriel and Mrs. Coulter. Despite this shock, Lyra quickly learns to read the alethiometer and understand its messages. Although her alethiometer enables her to discover the truth in everything around her, Lyra is unaware of the incredible role her own life plays in the fate of the universe. Lyra is the subject of a great prophecy in which she is destined to commit a fateful betrayal that will determine the future of all worlds.

To succeed in the rescue mission for the children, the gyptians enlist the alliances of three people who come to regard Lyra dearly: Serafina Pekkala, the witch queen who reveals that the fate of universe lies in Lyra's future; Lee Scoresby, a Texan aeronaut and commander of a hot air balloon; and Iorek Byrnison, a renegade armored polar bear, deposed as king of his clan by a deceitful brother. While on their long, hard journey in the far North, Lyra and Pantalaimon are kidnapped by hunters who take them to Bolvangar, the place where all the kidnapped children have been brought. At long last, Lyra is happily reunited with Roger, but to her horror, she witnesses intercision, the gruesome Dust experiment that separates child and dæmon. Banding together, the children and their daemons escape the terrors of Bolvangar, fleeing into the safety of the gyptians, Serafina Pekkala's witches, Lee Scoreby's balloon, and Iorek Byrnison.

Although the children are rescued, the journey for Lyra and Roger is far from over. They travel further north and finally find Lyra's father, Lord Asriel. Lord Asriel has experimented with Dust as well, and has discovered its role in crossing the barriers into other worlds. He has constructed a bridge to another world, but crossing that bridge requires the energy released in an intercision. Unable to sacrifice his own child, Lord Asriel makes Roger his prey and escapes to another world. The universe has been broken and Lyra's friend lies dead, but she vows get revenge and discover the secret of Dust.