After the events of Divergent, Beatrice "Tris" Prior, Tobias "Four" Eaton, Caleb Prior, Peter Hayes, and Marcus Eaton seek refuge in the Amity sector. Tris overhears Marcus and Amity leader Johanna Reyes discuss the fact that the Abnegation leaders died to protect secret information. Erudite and the Dauntless traitors arrive to arrest the Divergents, but Tris flees with Four, Caleb, and Susan Black on a train to the Factionless sector. There, they meet Tobias' mother, Evelyn Johnson-Eaton, who tries to persuade her son to sway Dauntless into joining forces with the Factionless against Erudite.
While Caleb and Susan return to Abnegation, Tris and Tobias head to Candor headquarters, where the other Dauntless now reside. Under truth serums, Tobias confides his reasons for transferring to Dauntless, and Tris reveals her killing of Will in self-defense, which strains her relationship with her friend Christina. That night, the Dauntless traitors, led by Eric, arrive and shoot simulation serums into their fellow Dauntless and knock everyone unconscious except the Divergents: Tris, Uriah Pedrad, and several others. As Eric begins executing the Divergents, Tris wounds him and allows the others to capture him as the remaining traitors flee. Their safety is revealed to be guaranteed by Erudite renegade and Will's sister, Cara.
Tris, Tobias, Lynn, and Shauna spy on the discussion arranged by the Candor leader Jack Kang with Jeanine Matthews's representative and Dauntless traitor, Max. Lynn shoots and kills Max, and Shauna is rendered paraplegic by a nerve serum. To prevent Jeanine from holding another prisoner exchange, the Dauntless vote to execute Eric, which Tobias does without hesitation. To avoid being dependent on Candor, the Dauntless return to their own headquarters and disable most of the security cameras inside. However, Tris is alerted by Christina that one camera has caused three Dauntless members (Marlene, Hector, and Kee) to become simulated into attempting suicide unless a Divergent is handed over. They are unable to save Marlene.
Tris surrenders to Erudite and is placed in a cell by Peter and, to her shock, Caleb, both of whom are working with Jeanine. Tobias follows and is captured but not before he convinces Dauntless to ally with the Factionless, with their insurgency arranged to occur several days. After unsuccessful simulation tests, Jeanine orders Tris' execution, but Peter swaps the lethal dose with a paralytic and frees Tobias, and the three escape to Abnegation. Tris meets with Marcus, who tells her that Jeanine has withheld Abnegation's secret. If the Factionless learned of it, it would certainly be destroyed.
Tris, Christina, and Marcus head for Amity to request Johanna's help. She, alongside several others including Susan's brother, Robert, choose to assist them, despite Amity's resistance. They are joined by Cara and another Erudite renegade, Fernando, who act as navigators. The "Insurgents" infiltrate Erudite headquarters. Fernando is killed, but they manage to access Jeanine's laboratory. Inside, Tris faces down simulations before she confronts Jeanine, who is cornered by Tori Wu. Tori kills Jeanine and then brands Tris a traitor. The invasion of Erudite over, Tris learns of the casualties, including Lynn, and the fact that the Factionless have taken all weapons to rule in Jeanine's place. Tris is handcuffed, alongside Christina, Marcus, and the other Insurgents, but manages to pass the information to Tobias, which he and Caleb share through the computers. The secret video, narrated by Edith Prior, from "an organization fighting for peace," reveals that the world had become corrupt, and the city was sealed to allow the Divergents to increase, and Amity was then to open the fence forever and allow the population to re-enter the world. The room erupts into voices as the book ends.
