A future dystopian Chicago has a society that defines its citizens by strict conformity to their social and personality-related affiliations with five different factions. That removes the threat of anyone exercising independent will and threatening the population's safety again by war or another human-created catastrophe. Those who fail the initiation of their particular faction are deemed Factionless and are treated as a lower class and a drain on society.
After the revelation about their city, Evelyn Johnson-Eaton becomes Chicago's leader, which forces all factions to live equally with the Factionless. Confessing their role in the insurgency, Beatrice "Tris" Prior, Christina, and Cara are pardoned. Tris learns from Tobias "Four" Eaton about the rebel "Allegiant," who work to restore the faction system. Several people are killed in a confrontation between faction members and the Factionless, including Evelyn's right-hand man, Edward. Tris is invited to a meeting with the Allegiant, whose leaders, Cara and Johanna Reyes, plan to usurp Evelyn and send envoys outside the city. Tris is selected for the expedition, alongside Tobias, Cara, Christina, Peter Hayes, Uriah Pedrad, and Tori Wu. Tris asks Tobias to free her brother Caleb from execution. Tori is killed by the Factionless, and the others escape and meet Tobias's mentor, Amar, who has long been presumed dead. They are taken to the Bureau of Genetic Welfare and its leader, David.
David explains that Chicago is walled off from the outside world in an experiment sanctioned by the US government to produce genetically-purer (GP) "Divergents" from the genetically-damaged (GD) population, the result of a failed attempt to correct human genes that led to the "Purity War." David gives Tris her mother Natalie's journal that details her life before Chicago. She was a refugee from Milwaukee who joined the Bureau and became a volunteer to stop Erudite's killing of Divergents. Those rescued included Amar and Tori's brother, George. Tobias learns he is not a true Divergent and joins GD Bureau member Nita in a rebellion against the GP staff. Tris is skeptical of the plan but jealous of Nita. The GP informant Matthew helps Nita access the Weapon Room and set off a bomb that causes Uriah to be brain-damaged. Tris stops Nita's rampage by holding David hostage before she wounds and arrests her.
Tris is appointed a council member and realizes that the Bureau supplied Erudite with the simulation serums that controlled Dauntless in the invasion of Abnegation. Security footage reveals that Marcus Eaton, who was banished by Evelyn, is working with Johanna to steal weapons from the Factionless, which Evelyn will counter by releasing the death serum. Tris learns that David intends to release serums that can erase the population's memories to save his experiment. She formulates a plan to release the memory serum on the Bureau while Tobias, Christina, and Peter, with Amar and George's help, return to Chicago with antiserums for Christina and Uriah's families.
Tobias, with his own plan to inject his mother with a memory serum, confronts her and asks her to avert the war in exchange for becoming his mother again. Evelyn agrees, negotiates peace with Johanna and Marcus, and exiles herself for two years, and Marcus vows never to lead Chicago. Tobias gives the memory serum to Peter, who intends to start anew.
Caleb volunteers to expose the memory serum, a suicide mission, but Tris replaces him. She successfully repels the death serum but is shot by David. Dying, Tris sees visions of her mother embracing her, before she succumbs to her wounds. Tobias, Christina, and Peter return to the Bureau and learn from Cara of Tris's death. In a deep depression, Tobias is about to drink the memory serum to erase his memories of Tris until Christina stops him. Uriah's brother, Ezekiel "Zeke", and his mother, Hana, are with Uriah as his life support is unplugged.
Two-and-a-half years later, Chicago is reopened and being rebuilt, and people co-exist regardless of gene purity. Tobias, now an assistant council member under Johanna, welcomes Evelyn back from her exile. To celebrate Choosing Day, he, Christina, Caleb, Zeke, Shauna, Cara, and Matthew ride a zip line from the Hancock Building, where Tobias scatters Tris's ashes and finally accepts her sacrifice.
