The head Builder and his assistant sit down. The head Builder says that people will need to stay in the city for about 200 years, and he’s crafted a box to house Instructions detailing how to leave the city. The box will stay with the mayor and will open at the appropriate time. Everything goes according to plan until the seventh mayor becomes ill and, believing the box contains a cure, tries to break into it. He dies before he can tell anyone about the box, so it ends up in the back of a closet. Eventually, it clicks open.
It’s Assignment Day of year 241 in the city of Ember, which is dark except for the light bulbs that illuminate it. Today, graduating students will receive the job assignments. 12-year-old Lina hopes to be a messenger so she can run, but when she pulls a slip from Mayor Cole’s bag, it reads “Pipeworks laborer.” Doon, Lina’s former friend, draws messenger and angrily spits that it’s a useless job in light of supply shortages and blackouts. Later, Doon offers to trade with Lina—he wants to be a Pipeworks laborer so he can see the generator. Lina is thrilled and runs home to tell Granny and Lina’s baby sister, Poppy. Granny and Poppy are all Lina has left, as her parents died two years ago. Upstairs in their cluttered apartment above Granny’s yarn shop, Lina thinks about a bright city she likes to draw. The Book of the City of Ember teaches that Ember is the only light in the dark world, but Lina still wishes that her imaginary city really existed.
Lina starts work the next day. In the afternoon, an odd-looking young man asks her to carry a message to Mayor Cole. It says that there’s a new delivery from Looper. At the Gathering Hall, Lina waits impatiently for the mayor. Bored, Lina wanders onto the roof. The head guard, Redge Stabmark, roughly escorts her off the roof and spits that curiosity leads to trouble. When Mayor Cole hears Lina’s message, he sends her off without putting her in the Prison Room. Earlier that morning, Doon arrived at the Pipeworks ready to do important work. He accepts his boots and slicker and follows a young woman named Arlin Froll down a long staircase. At the bottom, Doon comes face to face with the river, which is huge and fast. Arlin walks him to each end of the river and past the generator room before taking him to fix a burst pipe. During lunch, Doon heads back to the generator room and goes in. After watching for a minute, Doon suspects that no one knows how the generator actually works. At the end of the workday, a man who works on the generator confirms this. Later, at home, Doon hurls a shoe heel in anger, but it hits Doon’s father in the head as he enters the apartment. Doon tells his father about his day, but his father says simply that Doon should pay attention. He then asks about Doon’s worm, which Doon is keeping in a box to observe. It’s grown in the last few days.
A few weeks later, Lina finds Granny pulling stuffing out of the couch. She’s looking for something, but she doesn’t know what. Lina realizes that Granny forgot Poppy in the shop and rescues the scared, screaming toddler. The next morning, Lina asks her neighbor, Mrs. Murdo, to check in on Granny. At work, Lina carries a message to the head gardener, Clary, in the greenhouses at the edge of Ember. Lina relays the message—a shop owner wants extra potatoes and cabbage—but Clary says she can’t fulfill the order, as the potatoes are bad. They hear wailing and Clary sends Lina away, but Lina hides and watches as a young man named Sadge Merrall stumbles toward the greenhouses from the dark Unknown Regions beyond Ember. Lina joins Clary in comforting Sadge, who says that he was looking for something to help them, but it’s impossible to look without a moveable light. After Sadge leaves, Lina asks Clary if there’s really nothing out there. Clary pulls out a bean seed and says that it has life in it, but nobody knows exactly what life is. She puts the seed in a pot for Lina to grow.
Mrs. Murdo spends more time at Lina’s apartment. Lina loves this, as Mrs. Murdo is tidy and makes sure everything is taken care of. One day, Lina hears a rumor that one shop in town carries colored pencils. Though she knows she should buy Granny a coat instead, Lina takes Poppy with her to go look. Looper owns the shop and shows Lina the pencils. Lina puts Poppy down and feels intense hunger for the pencils. She selects two and pays the high price of $10. When Lina turns around, Poppy is gone. Lina rushes into the street, but the lights go out. Lina cries in fear. Finally, the lights come back on. Lina finds Poppy—Doon cared for her. Later, Lina feels like her pencils aren’t so beautiful, as they make her feel ashamed.
At a town meeting, Mayor Cole shouts about solutions, but people throw rocks and garbage at him. Mayor Cole’s words make Doon angry, as he doesn’t believe the mayor has any ideas. When Lina gets home, Granny is excavating a closet and Poppy is chewing paper next to an old metal box. Lina stops short when she sees that the paper is covered in perfect printing, the writing of the Builders. She takes the pieces of paper. They’re Instructions for something and she’s sure they’re important. The next day, Lina asks Captain Fleery to look at them. Captain Fleery, however, thinks it’s an old recipe and tells Lina to stop worrying—she’s a Believer and thus believes that the Builders will eventually save them. Lina next asks her friend Lizzie to look at the Instructions, but Lizzie is too caught up in talking about her boring job as a Supply Depot clerk and her new, older boyfriend. Lina decides that she should alert the mayor, so she writes him a note. When he doesn’t respond, Lina tries to decipher the writing herself. After some study, she realizes that the document refers to the river and the Pipeworks. She decides to ask Doon for help.
Doon spends his free time at work wandering. He finds only a locked supply closet and a ceiling hatch in a tunnel marked “No Entry.” There are also some rocks near the river that look like there’s writing on them, but he believes he’s never going to understand electricity or do anything important. One day, Doon decides to go to the library to research fire as a moveable light source, but fire only happens by accident in Ember. Lina catches him on his way out and asks him to look at her document. Doon agrees that it’s important and agrees to sneak Lina into the Pipeworks the next day to check out the locked door. In the Pipeworks, Lina insists that the door must be the door out of Ember—but they hide when they hear scraping, thuds, and a muffled voice. They catch a glimpse of a man and Doon is confused, as this person doesn’t work in the Pipeworks. Lina and Doon lament that this man got to the door before them and will be the hero for saving Ember.
The next morning, Granny wakes up ill. Lina cares for Granny for two days. On the third morning, Granny dies. Lina and Poppy spend the day at Mrs. Murdo’s, and Mrs. Murdo tells Lina that she and Poppy should move in with her. The next afternoon, Lina catches sight of Lizzie leaving the storeroom with a bag. Lizzie seems distracted and trips, spilling her cans. Lina picks up a can of peaches and one of creamed corn, foods she hasn’t had in years. Lizzie runs away. The next day, Lina catches Lizzie before work and gets her to admit that her boyfriend, Looper, finds things in supposedly empty storerooms and shares them with her. Lizzie says that it’s fine to take these things if Ember is dying anyway, but Lina insists it’s not fair or moral. She refuses Lizzie’s offer of more cans. A week later, Doon decides to check the odd door in the Pipeworks again. It’s unlocked and inside, Mayor Cole sits asleep, surrounded by food, clothes, and light bulbs. Doon shares this immediately with Lina, and they realize that Looper must be funneling supplies to Mayor Cole. They decide that since the mayor is the one committing the crime, they should tell the guards.
Lina seeks out Clary and asks her to come look at the Instructions. She tells Clary everything about Mayor Cole and the room in the Pipeworks. Clary sighs that there’s darkness everywhere in Ember, even inside the people. In people, the darkness manifests as greed. Clary also notes that Lina’s seed sprouted. When Clary looks at the Instructions, she suggests that the title is “Instructions for Egress”—Instructions to leave the city. Lina shares this with Doon and they decide to announce their discovery at the Singing celebration in two days. The next day, Doon sneaks Lina into the Pipeworks again. Following what they can read of the Instructions, they discover a ladder down to the river and a door. Inside are boxes marked “matches” and “candles,” and when Lina and Doon figure out that candles are moveable lights, they’re thrilled. Using the candles, they can see that the room contains hundreds of boats, which are supposed to float on the river and carry them out of Ember.
The next morning, Doon packs a bag for the journey and checks his worm. The worm had wrapped itself up but as Doon watches, a moth breaks out of the worm’s shell. On the street, Doon sees guards asking for him and full of rage, he runs to warn Lina. They find posters accusing them of spreading rumors and decide to hide in the school. They discuss whether they can still make their announcement at the Singing in a few hours, but there are always guards there. Doon suggests they leave someone a note and take a boat themselves. Lina is afraid to leave Poppy, but agrees to take Clary a note. Outside, however, guards capture Lina and take her to the Gathering Hall to see Mayor Cole. As Mayor Cole scolds Lina, the lights go out. Lina pushes through the dark onto the roof and joins in with the Singing from a hiding spot. The lights go out during the last song, but come on again right after. Lina joins the crowd, takes Poppy from Mrs. Murdo, and meets Doon at the Pipeworks. She shares that she knows now that Ember isn’t safe at all. Together, she and Doon wrestle a boat into the river, climb in, and untie it. They shoot down the river until they reach a pool where the river seems to end. There, they discover a book and realize that Lina forgot to give Mrs. Murdo their note. Since there’s no way to return to Ember, they hike up a path Lina discovers. There’s a sign from the Builders greeting them. After an hour or so, the air smells different and they come out onto a strange expanse lit by a silver orb. The ground is covered in hair. Exhausted, the three sit in silence and realize the silver orb is moving. They watch tearfully as the silver orb disappears and in its place, a bright one rises and illuminates the colorful world.
Lina and Doon turn to the book. The woman writes about her choice to participate in this experiment, which is intended to preserve humanity in the face of a disaster. She’s one of 100 older adults and 200 babies who take a bus and then climb down a steep path to a pool by the river. Motorboats will take them to their final destination. The babies are never supposed to know about the woman’s world, but the woman thinks that her account is important—someday, people will need to read it. Lina and Doon realize that they came from this place, though they can’t see any evidence of a disaster. They spend their day searching for a way back to Ember and eventually discover a cave. Inside, they find a ledge overlooking Ember far below. They tie up the letter in a rock and throw it down. Mrs. Murdo picks up the strange package that lands in front of her.
