Allegories: Adam and Eve
Will and Lyra’s journey into maturity is itself an allegory for the biblical story of Adam and Eve. There is even a prophesy proclaiming that Lyra will be a new Eve, and cause humanity to fall again, as they once did when Eve ate from the tree of knowledge and stained humanity with original sin. Their physical journey also mirrors that of Adam and Eve, with Lyra starting out comfortably in Oxford during the events of the Golden Compass, and being continually thrown into more dangerous and difficult situations as she learns and matures. This mirrors the struggles of Adam and Eve on earth when they were thrown from paradise. When Lyra makes the conscious decision to enter into a relationship with Will, Dust (an allegory itself for sin) returns to the world and settles, implying that Lyra did indeed cause another ‘fall’, but that this was not necessarily a bad thing.
Motifs: Destiny/Fate
Destiny is a much-used motif in The Amber Spyglass, and both Will and Lyra have destinies that have been following them since the last two novels. According to a prophesy, Lyra is to be a new Eve and cause humanity to fall again, and Will is the bearer of the subtle knife, giving him his own dark destiny. Indeed, the central conflict between Lord Asriel’s forces and the church revolves around destiny, with one side seeking to destroy it and let all be free to choose their own paths, and the other seeking to adhere to it strictly.
Symbols: Daemons
Throughout the trilogy, daemons are a symbol for individuals' souls. This is seen in The Golden Compass, when the reader is introduced to the concept of daemons, who take form depending on their human counterpart’s personalities, and cannot be far from them without causing great discomfort to both. It becomes all the more evident in The Amber Spyglass, when Lyra and Will are forced to leave their daemons behind, and Will discovers that he does indeed have a daemon (who then becomes physical, rather than existing in his soul).