As a new Initiate with the Alchemists' Council, Jaden is trained to maintain the elemental balance of the world, while fending off interference by the malevolent Rebel Branch. Bees are disappearing from the pages of the ancient manuscripts in Council dimension and from the outside world, threatening its very existence. Jaden navigates alchemy's complexities, but the more she learns, the more she begins to question Council practices. Erasure — a procedure designed not only to remove individuals from Council dimension but also from the memories of other alchemists — troubles Jaden, and she uses her ingenuity to remember one of the erased people. In doing so, she realizes the Rebel Branch might not be the enemy she was taught to fight against.

Jaden is caught between her responsibility to the Council and her growing allegiance to the rebels, as the Council finds itself at the brink of war. She is faced with an ethical dilemma involving the free will of all humanity and must decide whether or not she can save the worlds.