As Earth is being ravaged by a series of apocalyptic events known as the Disaster, a coalition of architects, scientists, and doctors (called the Builders) create an underground city named Ember, with an initial population of 200 citizens (100 elderly adults, 100 babies), to ensure humanity survives, with the intention that future generations of the city will not know about the outside world or that they live underground. They build the city to last for two centuries, after which the citizens of Ember will evacuate and return to the surface world. The Builders give the first mayor of the city a box with a timed lock set to open after 200 years, containing instructions explaining how to leave Ember. The box is passed successfully from mayor to mayor, until the seventh mayor who, thinking it could contain a cure for the deadly coughing disease he contracted, takes the box home and tries multiple times to break it open, but fails. He then dies before he can return the box to its rightful place or inform the next mayor of its importance.

Approximately two hundred and forty-one years after Ember was established, the city's supplies are in danger of exhaustion, and its hydroelectric generator is in decay, causing the power to go out intermittently. At their graduation ceremony, young people are assigned jobs by lottery: Lina Mayfleet is assigned the job of "Pipeworks Laborer" and Doon Harrow is given the job of "Messenger". However, both are displeased with their assigned jobs so they exchange their assignments and begin work in their respective positions. It is revealed that the seventh mayor was Lina's great-great-grandfather, and because of that, the box is actually in their own home. By now the timer has finished counting down and the lock has clicked open. When searching the closet, Lina's grandmother finds the box but tosses it aside, not realizing its importance. The opened box is found by Lina's baby sister, Poppy. When Lina comes home, she finds Poppy with torn pieces of paper in her hands and mouth. By the time Lina managed to get the paper from Poppy, they had already been mostly destroyed. After examining the paper, she decides that its contents had been written by the Builders due to its writing style. Using some glue, Lina reassembles the message as best she can. There are many gaps and some words make no sense, so it proves difficult for Lina to completely salvage the writing. With the help of her friend Doon and her late father's friend Clary, she starts to piece together the writing. They discover that the title of this document is "Instructions for Egress", and presume that the document must show the way out of Ember. After much trial and error, they eventually manage to decipher most of the document. The instructions lead to a hidden room built on the side of the river that flows underground throughout the city in the Pipeworks, an underground network of tunnels that carried the plumbing pipes of the city. The room contained hundreds of boats, matches, and candles to create portable light, something never successfully created in Ember. The builders meant for the citizens of Ember to board these boats and be carried down the river into the outside world.

Lina's grandmother dies shortly after their discovery of the document, and Lina and Poppy move in with a neighbor, Mrs. Murdo. At work, Doon discovers that the mayor of Ember and a storeroom worker named Looper have been stealing supplies, and he and Lina report the crime to the guards, who unknown to them, are also corrupt. Instead of arresting the mayor, they learn that the guards have declared them criminals and there are notices everywhere with their names. Doon and Lina plan to escape Ember in the boats and agree to meet in the Pipeworks at a certain time, but just before, Lina is arrested and taken to the mayor, who plans to throw her in jail. Suddenly, a blackout occurs, allowing her to escape without being seen; she meets Doon in the Pipeworks with her sister Poppy in tow. Lina, Doon, and Poppy escape in a boat through the river, its current carrying them forward. When the boat stops, they learn the origin of Ember from a diary left by one of its original colonists. Shortly after they are faced with a very steep climb and emerge onto the surface. After exploring the above world, they find a tunnel with a steep drop into a cave. Below, they see Ember's lights and realize they had lived underground for years. To alert the rest of the city about how to leave Ember, they throw a packet with a letter detailing the path to exit, down to the center of Ember. The packet is found by Mrs. Murdo on Harken Square.

The City of Ember was praised for its setting and main characters, Lina Mayfleet and Doon Harrow. Kirkus Reviews praised the characters, stating: "The likable protagonists are not only courageous but also believably flawed by human pride, their weaknesses often complementing each other in interesting ways."^[3] Sally Estes from Booklist commented how readers would be able to connect to Lina and Doon's courage amidst the conflicts.^[4] Robert Sutton from Horn Book Magazine compared the novel to Gathering Blue by Lois Lowry, noting how "the darkness of Ember is essentially literal" with the generator (the mechanical light operator) failing and running out of power, leading to frequent blackouts. Sutton noted how DuPrau does not explain the history of Ember all at once, which would confuse and overwhelm the reader and instead, "allows the events of the story to convey the necessary information". Lina and Doon were described as "good sorts" that are "deeply etched".^[5] Dian Roback from Publishers Weekly also praised the "full blooded characters" as every bit as good as the plot which would hook readers until the end.^[6] Although Jones Johns from School Library Journal wrote that the setting was not as ingenious as the ones in Joan Aiken's Is and Lois Lowry's The Giver, he said that the characters and pace of the plot would keep readers hooked.^[7]

A film adaptation of the novel, directed by Gil Kenan, was produced by Walden Media and Playtone with Bill Murray as the mayor, Saoirse Ronan as Lina, and Harry Treadaway as Doon.^[8] Filming was finished in October 2007, and the film was released in theaters a year later on October 10, 2008. City of Ember was released on DVD on January 20, 2009. The film received mixed reviews, with a Metacritic rating of 58/100, indicating "mixed or average reviews".^[9]

• 2003 Child Magazine's Best Children's Book
• 2003 Kirkus Editor's Choice
• 2006 Mark Twain Award^[10]
• 2006 William Allen White Children's Book Award
• American Library Association Notable Book

• Jeanne DuPrau's website Archived February 27, 2019, at the Wayback Machine