Meet Lina and Doon. They're your average twelve-year-olds, except for the fact that they live in the city of Ember, and lead lives that couldn't be more different from your own. Since they're graduating from school, they and their classmates are all assigned jobs. Lina draws a job in the underground Pipeworks, when she'd really wanted to become a Messenger. Doon offers to trade with her, and soon enough, she's gallivanting around town, delivering messages like nobody's business.
Her job puts her ear right up to the grapevine, so while she's out and about in town, Lina gets the skinny on all the goings on. She learns that all the citizens are afraid that the lights will go out for good, and that the food stores are dwindling. Meanwhile Doon, down in the Pipeworks, learns that the generator which powers the city is slowly degrading, and no one knows how to fix it. This stuff is a big deal because Ember is surrounded by darkness, and there's no way out of the city—nowhere to go if the lights fail or the food runs out. Yeah, this is not good.
Things aren't good on the domestic front, either. Lina's grandmother is supposed to be looking after her baby sister, Poppy, but she's starting to go senile and isn't much help with the kiddo. To make matters worse, Granny's obsessed with finding something her grandfather, a former mayor of Ember, had stored away. When a mysterious box surfaces in their home, Lina thinks its contents might be helpful in handling the city's current situation. There's just one problem: Poppy has already chewed on the paper inside.
With Doon's help, Lina figures out that the paper contains instructions for the city's Builders on how exactly to exit the city and head for safety when the time comes. The kids also discover that the mayor, aided by an unscrupulous clerk named Looper, is stealing and hoarding rations. When the mayor tries to have the kids arrested for their accusations, Lina and Doon have a decision to make: what should they do with their information about how to leave the city?
In the end, they opt to take a chance and get the heck out of Dodge. They head out into the darkness with Poppy in tow, and plan to leave directions on how to exit the city for the other residents to find. After a trip by river, they ascend to the outside world, and discover that Ember has actually been underground this whole time. They also discover a journal written by one of the first residents of Ember, which warns of impending disaster and calls the city a last resort. There's definitely more to this story.
Seeing the sunrise for the first time is mind-blowing. And trees—who knew the natural world was so beautiful? The kids stumble upon a crevice and throw their directions down into the city below. Mrs. Murdo, who has been taking care of Lina and Poppy since Granny's death, finds the instructions, but that's where it all ends, leaving us to wonder what will happen next.