Dr. Mary Malone was a physicist who was investigating dark matter, and was told she must play the part of the Serpent for the second Adam and Eve. She was a former nun, having become an atheist after an encounter with a man from Italy and the taste of marzipan reminded her of her first romantic encounter.
Lyra Belacqua, upon arriving in Will's world, meets Mary when she tries to find an "experimental theologian" (physicist) in hopes of discovering more about Dust. Mary is amazed by Lyra's knowledge of dark matter, especially after Lyra demonstrates her ability to speak of the unknown by use of the alethiometer.
Mary, inspired by Lyra's abilities, uses the supercomputer she and her colleague, Dr. Oliver Payne, designed to communicate with Dust. The Dust consequently tells Mary to travel from her own world, through the window that Will found at the beginning of The Subtle Knife. The Dust tells her through words on the computer screen that she is supposed to "play the Serpent". The Dust also tells her about the journey she is about to embark on and warns her to destroy the computer before she leaves. Mary travels through Cittàgazze to yet another world, where she will eventually become the Serpent. She spends most of The Amber Spyglass with creatures known as the Mulefa, trying to see the Dust, which the Mulefa can do naturally. This leads to the creation of her "Amber Spyglass".
At the end of the third novel, the witch Serafina Pekkala reveals to Mary both how to see her dæmon and also its form - that of an Alpine chough. She offers to help Will upon his return to his own world.