Themes are the fundamental and often universal ideas explored in a literary work.
The battle between Metatron’s forces and Lord Asriel’s forces ultimately boils down to the human struggle for free will. Metatron and his minions in the Church want to control human destiny and enforce their rules on all the conscious beings of all the worlds. Lord Asriel and his forces want to create a world in which free will is protected, a world in which all thinking beings are allowed to choose the course of their own lives.
In the Judeo-Christian tradition, grace is the sanctification God grants to some people. Like Adam and Eve, who exist in a state of grace before the Fall, Lyra exists in a state of grace until Lord Asriel’s battle. She reads the alethiometer with the help of grace until Lord Asriel’s battle is won and Lyra realizes that she is in love with Will. After Lyra grows up, she has to learn how to read the alethiometer like everyone else. This is because free will has triumphed over destiny. Because Lyra “fell”—grew up, started craving knowledge—people gained the right to decide how they want to live. In Pullman’s world, this right is very desirable, but it does mean that everyone has to live without grace and without the comfort and protection of a higher power.
The most offensive thing about the Church in His Dark Materials is its relentless quest to ensure ignorance. Beginning with Adam and Eve and the forbidden tree of knowledge, God and the Church have sought to prevent people from becoming freethinking adults by trying to restrict knowledge. When Adam and Eve defied God and took from the tree, they abandoned the state of innocence and became free adults who suffered and toiled, but who at least thought for themselves. For some characters in Pullman’s trilogy, like Lord Asriel, the witches, and the mulefa, Adam and Eve’s fall was the beginning of good in the world. For the authorities of the Church, the Fall signaled the ruin of humanity. The Church would have preferred it if people dwelled in the state of innocent ignorance forever. Lord Asriel and his compatriots stage their rebellion to ensure that everyone has the right to attain knowledge and become a freethinking adult.
Metaphorically, the first human sexual encounter occurred when Eve told Adam to eat from the fruit of the tree of knowledge. From the very beginning, then, sex and knowledge have been intertwined. The Church of Pullman’s fiction particularly objects to sexual knowledge and seeks to curtail sexual activity in an attempt to prevent adults from becoming independent thinkers. Lyra’s “fall”—the proto-sexual encounter she has with Will in the world of the mulefa—badly damages the aims of the Church. In engaging in a sexual relationship with Will, Lyra chooses to grow up and abandon the innocence of her childhood. Because Lyra’s destiny is to put an end to all destiny, her choice to express physically her love for Will restores Dust to the world and ensures that the Church will be defeated. After Lyra’s decision, everyone will have the right to mature and make independent decisions without fearing the censure of the Church.