This volume concludes the trilogy and begins with Mrs Coulter holding Lyra hostage having apparently had a change of heart toward her and now is not intent upon killing her but saving her. The two hide-out in a remote cave. Balthamos and Baruch, the angels, are intent upon conveying Will to Lord Asriel, but he's going nowhere until he's found Lyra.
The Magisterium is after physicist Mary Malone, sending an assassin to track and eventually kill her after she's led him to Lyra. Mary finds her way through a window between worlds and ends up in a weird place where the dominant species are in many ways rather elephantine creatures which use disk-like seed pods for traveling on natural roads, using the tree oil to lubricate these pod wheels. Mary makes her home in this world for a while and studies the people and the trees, discovering that the dust, leaking between worlds, is causing issues. It is she who invents the amber spyglass.
Will meanwhile has persuaded Iorek Byrnison to help him rescue Lyra. After this occurs they have one of the strangest adventures, wherein Will and Lyra and a couple of others have to visit the world of the dead, and this means leaving their dæmons behind, which is exceedingly painful to them, but they succeed in this heroic quest and survive. This changes Lyra's relationship with Pan, and the two of them can now be further apart than ever they were able before, without enduring the intense pain a separation normally causes. They then have to battle the ghost-like Gallivespians, and they do this by luring them into the world where Mary was hanging out, wand where the Gallivespians cannot survive.
Will and Lyra are now in love as evidenced by the cavorting of their dæmons, but it's a love that's destined to be denied, because they neither of them can survive indefinitely outside of their own world, and so are forced to separate for the rest of their lives, unable even to open a window, because of the leaking Dust problem. Despite this sad ending, I still commend this as a worthy read!