Much of the conflict in The City of Ember comes from keeping secrets. DuPrau’s use of a prologue device in the viewpoint of a third-person omniscient narrator makes the reader privy to the chief builder’s plan for the secret Instructions, resulting in reader suspense and dramatic irony that lasts for most of the book. Readers know far more about Ember and the Instructions, at first, than any of the living inhabitants. For example, the reader exclusively knows the reason why the crucial Instructions were in Granny’s closet—but DuPrau ensures that her readers do not know everything, portraying secrets in the novel as mysteries that require cooperation and trust to solve.

Lina and Doon make their discoveries and surpass even the reader’s knowledge of Ember’s past by working together. While working on the larger secret of what the Instructions might contain, they compile their information gleaned from Lina’s friend Lizzie and Doon’s off-hours Pipeworks explorations. First, they establish that someone can get into the locked room in Tunnel 351—whose secrecy frustrates Lina: “As if he’d found something! What was it! I can’t stand not to know!” (130). Later, they learn the extent of the deceit: “The mayor has a secret treasure room in the Pipeworks” (158).