"The Amber Spyglass" picks up right where the second book ends. While Lyra is kept captive by Mrs. Coulter, the Magisterium is trying to find her to kill her and prevent the fall of humanity. Will, meanwhile, finds Lord Asriel, who is planning war against the Magisterium, and Lyra's physicist ally, Mary Malone, is stalked by an agent of the Magisterium and enters another world. Will is able to rescue Lyra, but while she was unconscious, she met Roger's spirit in the world of the dead and promised to help him.
Will and Lyra are able to strike a deal in the land of the dead to let the dead escape and be reintegrated into the fabric of the universe. When they return, a great battle ensues, with the forces of Asriel, Coulter, Will, Lyra, and their allies against the Authority and the angel Metatron.
Coulter and Asriel are destroyed while taking down Metatron, and Lyra and Will are able to find their daemons and escape into another world. After they share a first kiss, they learn that the openings between worlds are allowing Dust to escape, which creates Spectres. All windows must be closed except for one, and instead of leaving the window between their worlds open so they can be together, they choose to leave the one open for the dead, then Will breaks the knife. They make a pact to go to the same place every year to think of each other. Lyra loses the instinctive ability to read the alethiometer but decides to study it properly.
