In a futuristic Chicago, society is divided into five factions based on human virtues. Following the events of the previous story, the faction-based system is crumbling due to a violent coup d'état led by the Erudite faction seeking control. Beatrice "Tris" Prior, a Divergent who does not fit into any one faction, is on the run with her partner Four, her brother Caleb, and fellow Dauntless member Peter. They seek refuge in the peaceful Amity faction, but their peace is short-lived as they are pursued by Jeanine Matthews, the ruthless leader of Erudite, who is determined to exterminate all Divergents.

As they are flushed out of hiding, the group encounters the Factionless, a band of individuals who don't belong to any faction and who have their own plans for the city. Tris and her companions must navigate the Factionless and other risks to find allies in their struggle against Erudite. Meanwhile, Jeanine has come into possession of a mysterious box containing a message from the city's founders, the contents of which can only be accessed by a Divergent. This places Tris at the center of her scheme, forcing her to confront her inner demons and past decisions while sparking a race against time to stop Jeanine from unleashing further destruction.