Sixteen-year-old Beatrice Prior lives in a dystopian, futuristic Chicago that segregates most individuals into one of five factions. Those outside of these factions are classified as factionless and are consigned to the outskirts of civilization. As the story begins, Beatrice is preparing for the aptitude tests that will decide whether she belongs to Abnegation, Amity, Candor, Dauntless, or Erudite. Her brother, Caleb, faces the same challenge. The aptitude tests consist of a series of simulations that determine a young initiate's suitability for one of the factions. Beatrice's test is administered by Tori, who classifies her as divergent. In Beatrice's world, divergents live in fear of discovery and subsequent annihilation.

At the Choosing Ceremony, Beatrice opts for Dauntless, while Caleb declares for Erudite. Beatrice's father, Andrew, is furious, but her mother, Natalie, is supportive of the siblings' choices. After the Choosing Ceremony, Beatrice joins the other initiates on the train to Dauntless headquarters. There, she reinvents herself as Tris. Her closest allies are Will (an Erudite transfer) and Christina and Al (two Candor transfers). At the beginning of the initiation process, the recruits are divided into two groups. The Dauntless-born initiates answer to Lauren, while the transfers answer to Four. The head of all the trainers is Eric, an arrogant bully who equates merciless ferocity with courage. He informs everyone that the initiate process will be divided into three stages and that initiates will be ranked according to their accomplishments; those who fail to make the top ten will be declared factionless.

The first stage of initiation consists of hand-to-hand combat. Four prepares the recruits by teaching them self-defense and weapons techniques. This is a difficult stage for Tris, as her small build makes her an easy target. Molly, Peter, and Drew (a trio of Candor transfers) are Tris's primary tormentors, both in and out of the ring. Despite her own trials, Tris stands up for Al during a knife-throwing exercise. For the second stage of initiation, the recruits are injected with a serum that generates frightening simulations in the mind. To exit the simulations, initiates must stabilize their breathing and heart rates through sheer will. Meanwhile, Tris impresses Four with her ability to exit her simulations faster than anyone else. Four eventually deduces that Tris is divergent and warns her against revealing her secret. Because of her divergent abilities, Tris places first. Meanwhile, Al finishes last and is disheartened; he joins Peter and Drew in attacking Tris. It is Four who saves Tris from the hands of her tormentors. Later, Al tries to apologize to Tris but is rebuffed. Distraught, Al commits suicide.

Tris is burdened with guilt, but Four warns her that greater dangers await her. Meanwhile, Tris begins developing an attraction to Four. Before Stage Three commences, Four invites Tris into his personal fear landscape. The fear landscape is the most difficult of the three stages, and each initiate's landscape is unique to the individual. Inside Four's landscape, Tris discovers that one of his four fears is Marcus Eaton. From this, Tris deduces that Four is really Tobias Eaton, the son of Marcus Eaton, one of the Abnegation council leaders. After the shared experience, Four declares his attraction to Tris, and they form a romantic relationship. Their new alliance is tested, however, when Tris panics during a fear landscape exercise and abruptly exits the simulation. Subsequently, Four humiliates Tris when he berates her in front of everyone. Angry, Tris takes a trip to Erudite headquarters.

There, she has an emotional reunion with Caleb, but their conversation is fraught with tension. Before she leaves, Tris is taken to Jeanine Matthews, the Erudite representative, and interrogated. Jeanine tries to probe Tris for evidence of her divergence but does not succeed in uncovering her secret. Upon her return, Four ominously reveals that he has seen Erudite’s plans to wage war against Abnegation.

On Initiation Day, Tris passes her fear landscape test and earns the top spot. Later, while kissing Four, Tris experiences an epiphany: Erudite's plan to use a Dauntless army against Abnegation will be facilitated by a simulation-inducing transmitter serum. Tris remembers that this serum was injected into new Dauntless members on Initiation Day. That night, Dauntless soldiers awake in a stupor and march to the Pit to pick up weapons. The soldiers then take the train to the Abnegation sector, where they begin executing Abnegation civilians. On the train, Tobias finds Tris and clasps her hand, revealing his own divergence. The two are eventually forced to break their cover, however, when Tris shoots Eric in the foot to prevent him from killing Tobias. Both Tris and Tobias are taken to Jeanine, who injects Tobias with a specially designed serum for divergents. Jeanine then locks Tobias in the control room to monitor the simulation program, and Tris is knocked unconscious by a soldier.

Tris awakes in a tank that is slowly filling up with water. She prepares to die but is rescued by her mother. Natalie and Tris manage to exit the Abnegation compound, but Natalie is gunned down during the escape and dies. Tris eventually reunites with her father, Andrew, and her brother, Caleb, at the Abnegation hideout. There, Tris strongly advocates for the destruction of the computers that are running the simulation program. After much discussion, Tris, Caleb, Andrew, and Marcus take the train to Dauntless headquarters. There, they are ambushed by Peter, but Tris overpowers him. Peter later agrees to reveal the location of the control room in exchange for his safety. On the ground floor, Tris orders Peter, Marcus, and Caleb to stay behind as lookouts while she and Andrew make their way to the control room on the eighth floor of the glass building. As the elevator doors open onto the eighth floor, guards fire at Tris and her father. In the shootout, Andrew is killed.

Tris makes her way to the control room. There she battles Tobias, who eventually wakes up from his stupor and stops the simulation. Before leaving, Tobias retrieves the computer hard drive and hands it to Tris. On the train to Amity, Tris examines the hard drive and is disconcerted when she notes Marcus's interest in the same object. With a pang, Tris realizes that life is about to get more complicated and that the future is uncertain.