The Amber Spyglass functions as a conclusion to a larger Christian allegorical story: Lyra, who began the series as a child, must travel through her own Garden of Eden archetype in order to fulfill her destiny and establish free will. The main conflict between the Church, the Angels, and Lyra and her comrades symbolizes the real human struggle for enlightenment and free will.
Lyra's journey begins with her unconscious in a cave, with Mrs. Coulter keeping her poisoned and sleeping. Will arrives to free her, and together, the two of them leave their daemons behind and enter the world of the dead to lead all the ghosts to freedom. This portion of their journey is meant to force Lyra to leave her childhood behind: she departs without her childhood companion, Pan, and follows Will, who she soon realizes she is in love with. When they realize they do love each other, thanks to Mary, who acts as a serpent figure, the Dust slows in its escape. Now, Lyra finds it strange to appear naked before Will when they bathe in the river, symbolizing her transition to adulthood. She also can no longer read the alethiometer. This maturity comes with a responsibility: the two must separate in order to stop the Dust from escaping, exposing them both to the hardship of adulthood.
The Church in Pullman's society represents the ignorance of the garden; though it seems peaceful and orderly at first, human nature drives those under it to rebel and learn more, showing the church's more sinister side. Mary is a product of this ignorance: once a devoted nun within the church, she acts as Will and Lyra's own serpent when she exposes them to the idea of love and drives them out of their own innocence. When the hole is closed, Lyra learns that the church all but collapses, and resolves to study to relearn to read the alethiometer, as she and Will fought to be able to do. Her struggle symbolizes the human need to pursue knowledge, thus resolving the concept of original sin as a facet of human nature.
