In a future America, seventeen-year-old Jenna Fox awakes from a year-long coma with no memory of her family or her past. She remembers the darkness of her coma, but not the terrible accident that caused it. Her mother encourages her to watch home movies to jog her memory. Her father, a rich doctor and head of a medical research corporation, is usually away on business. Lily, Jenna’s grandmother, is strangely cold towards Jenna. Jenna attempts to reconstruct her world by reading the dictionary and watching the many home videos taken of her childhood. Against Mother’s instructions, she eventually ventures outside the house and meets her neighbor, an artist named Mr. Bender. On her walk back home, she falls into a shallow creek, and recalls her first memory from her past: nearly drowning as a young toddler.

Lily takes Jenna to the local Catholic mission, where Jenna sees a boy her age with black hair. That night, Jenna asks to be allowed to go back to school. Mother refuses, but at Lily’s insistence, eventually relents, allowing Jenna to register for a small, local school. On her way to visit Mr. Bender again, Jenna meets a strangely hypnotic boy named Dane. When Jenna arrives for her first day at school, she discovers that both Dane and the black-haired boy from the mission, Ethan, are students there as well. Though she worries about fitting in, Ethan and another classmate, Allys, quickly take Jenna under their wing. Allys, an amputee with prosthetic arms and legs, quickly decides she likes Jenna. Ethan warns her to stay away from Dane, while Dane warns her to stay away from Ethan. Jenna is assigned to work on a volunteer project with Ethan, and finds herself growing attracted to him.

On their way back from the mission, Ethan and Jenna pick up Allys at her volunteer project, which is at a hospital. Allys is an advocate for government oversight over medical procedures--something Allys believes would have saved her arms and legs. Allys mentions a product called Bio Gel, and Jenna realizes that her father’s company invented the product. Bio Gel can be used to create artificial human organs, though such creation is highly regulated. Jenna finds a hidden, locked closet in her parents’ bedroom along with a key, but before she can investigate, Ethan shows up at her door. He reveals that he spent a year in a juvenile detention facility for beating a man up. Touched by his honesty, Jenna kisses him. Lily tries to convince Jenna that a relationship with Ethan would be unethical, though Jenna does not understand why. At the next opportunity, Jenna breaks into the locked closet. There, she finds three computers, and attempts to pull the one with her name on it off its stand. One of the brackets slices her hand open, and Jenna is horrified to find that under her skin is not blood, but a layer of blue Bio Gel.

Jenna confronts her mother. Mother explains that Jenna’s hand, along with the rest of her body, was horribly burned during an accident. Only 10% of Jenna’s brain was able to be saved. The rest was reconstructed with Bio Gel. Jenna is horrified. Father arrives home the next day and attempts to provide more details. Jenna was dying despite medical intervention, and he and Mother had to decide to save her the only way they could, through Bio Gel. The use of so much Bio Gel is illegal, so they had to secretly transport her from Boston to California. Her entire body was recreated exactly using the home videos. Though Father sees this as a scientific miracle, Jenna only wants to know where he put her soul. Father and Mother beg Jenna not to tell anyone her secret.

Later on, Jenna tries to look up news articles about her accident, but her access is blocked. She talks with Lily, who hints that Jenna has been programmed to obey certain orders from her parents. Jenna tests it out, and discovers Lily was right. Feeling lost, Jenna goes to visit the church at the mission, where she sees Ethan. Ethan is confused and upset that she has been ignoring him ever since their kiss. Jenna reveals her secret to him, expecting him to reject her, but he does not. He tells her that the man he attacked was a drug dealer, who was selling drugs to Ethan’s brother. He warns Jenna not to tell Allys about her artificial body, as Allys will surely report her. Jenna visits Mr. Bender to use his computer and discovers her accident was caused when she, an unlicensed driver, drove her father’s car off a cliff, killing her two closest friends, Kara and Locke. Jenna sneaks into the hidden closet again and discovers that the computers are not computers at all—they are backups of brains. There is one for her, one for Locke, and one for Kara. Her parents explain that Locke and Kara’s brains could be used to testify for Jenna in a criminal trial. Jenna knows she must save Locke and Kara from the limbo-like hell they’re in.

During a conversation with Jenna, Allys pieces together that Jenna is the daughter of the Bio Gel inventor, a girl who was not supposed to survive a fatal car accident. Ethan worries that Allys will report Jenna. On her way to visit Mr. Bender, Jenna is attacked by Dane, who is revealed to be a sociopath, but fights him off. That night, Jenna finally remembers the accident, and that it was Kara, not Jenna, who drove the car off the cliff. Ethan and Jenna go to visit Allys, who has been absent from school, and discover that her infection has returned and that she is near death. Allys has told her parents to report Jenna. Later that day, after overhearing her father tell his security advisor that the brain backups will be moved the next day, Lily and Jenna plot together to destroy the backups. Jenna creates a diversion, allowing Lily to lock Mother and Father in Jenna’s room. Jenna throws all three backups into the pond. Mother and Father are upset, but ultimately understand Jenna’s choice. Early in the morning, Allys’ parents arrive at the doorstep and beg for Father’s help in saving their daughter.

Two hundred and sixty years later, Jenna and Allys are still alive. She lives at Mr. Bender’s old house. Jenna spent seventy years with Ethan, and now, many years after his death, arranged for their child to be born through a surrogate. Kayla, Jenna’s daughter, arrives home from school. Jenna finally understands the lengths a parent would go to for their child. Together, she and Kayla feed the birds.