The Builders create Ember and entrust exit instructions to a timed box. Two hundred and forty-one years later, Lina and Doon face Assignment Day, trade jobs, and begin to see the cracks in their underground world.

Lina begins her messenger routes and discovers the fragmentary document. Doon enters the Pipeworks and confronts the failing generator. Both begin to suspect that Ember's problems have no official solution.

Doon discovers Mayor Cole's hidden storeroom of hoarded supplies. Lina brings the fragmented instructions to the mayor, who dismisses her. The corruption at Ember's center becomes undeniable.

Lina and Doon collaborate to decode the instructions. They share their discoveries — the exit route and the mayor's corruption — and resolve to find the way out of Ember themselves.

Lina and Doon attempt to expose the mayor's corruption. The mayor retaliates by declaring them criminals. They go into hiding as the city's infrastructure deteriorates further.

Lina and Doon follow the Builders' instructions through the Pipeworks, find the boats left for them, and navigate the underground river with Poppy. The journey is terrifying and uncertain.

Lina, Doon, and Poppy emerge from underground and experience the natural world for the first time — stars, dawn, sky, grass, and sunlight.

Lina and Doon look down from a ledge and see Ember far below — a tiny cluster of lights in a vast cavern. Lina writes a message describing the way out and drops it toward the city, hoping someone will find it.