Many Chicago citizens run toward the wall, but soldiers under Evelyn (Naomi Watts) are told to shut down the perimeter, and thus, no one is allowed through. Evelyn directs Jack Kang (Daniel Dae Kim) of Candor to hold trials for the Erudite and Dauntless conspirators, in which a number of them become executions, starting with Max (Mekhi Phifer). Evelyn and Johanna (Octavia Spencer) attempt to pressure Tris (Shailene Woodley) and Four (Theo James) into taking leadership positions in the new coalition, but both refuse. After seeing that the hostile situation within the city is only going to get worse, Tris escapes with Four, Caleb (Ansel Elgort), Christina (Zoë Kravitz), Tori (Maggie Q), and Peter (Miles Teller) to journey beyond the wall that encloses Chicago. However, Tori is killed by Edgar (Jonny Weston) in the attempt.
The group is ambushed by Edgar, who is later disabled by an armed group of individuals and airships. The soldiers take the group to the Bureau of Genetic Welfare, a highly advanced city where they learn that years ago the government believed that society’s problems were caused by “damaged genes”. In an attempt to create a better society, they began to modify people’s genes, with disastrous results. The government set up “experiments” in an attempt to repair this mistake, establishing isolated cities across the remains of the United States. The hope is to raise enough genetically pure Divergent individuals to fix the “genetic damage” left in the wake of the Purity War.
Tris and Four are tested by Matthew (Bill Skarsgård) and Nita (Nadia Hilker) to verify and study their Divergence. Tris is shown to be truly Divergent, but Four’s genetic structure indicates that his genes are still “damaged”. Caleb and Peter are assigned to surveillance teams that monitor Chicago. Matthew then brings Tris to the leader of the Bureau, David (Jeff Daniels). David gives Tris a device that allows her to view her mother’s memories, and sees that her mother was rescued and adopted by the Bureau before volunteering to join the Chicago experiment out of dedication to the project. In return for his help in restoring peace to Chicago, Tris agrees to help David, who claims that only the council he reports to have the power to intervene.
Meanwhile, Four and Christina train with Nita and join the Bureau’s military force. They join the military on a rescue mission to a nearby wasteland village, though Four becomes mistrusting of the Bureau’s intentions after realizing that they are going there to kidnap and forcefully integrate children into the Bureau’s populace. Upon their return, Four discreetly petitions Caleb to keep an eye on the situation in Chicago. Four also attempts to warn Tris of the Bureau’s intentions, but she rejects his ideas.
Caleb warns Four of a rapidly escalating conflict back in Chicago between Johanna’s group of Allegiants and Evelyn’s factionless, with open war becoming an imminent threat. Four appeals to Tris for her to return to Chicago with him to end the bloodshed, but she decides to go with David to Providence to meet with the council. David agrees to reinsert Four back in Chicago, escorted by Matthew and some Bureau soldiers. Once in the air, Matthew quietly reveals to Four that the flight is a trap and he is meant to be killed. A skirmish breaks out and Four defeats all of the soldiers, though the airship crashes as a result. Matthew betrays David by helping Four get through the cloak wall. Four proceeds to Chicago while Matthew remains behind to be rescued by the Bureau and warn Tris.
Meanwhile, Tris and David meet with the council. Tris disagrees with the council’s objectives and criticizes how they have done nothing to stop the violence in Chicago. The council responds that David had the power to intervene whenever he desires, revealing that he has lied to her from the beginning. During the return flight to the Bureau, Tris ends their partnership. Upon her return, she gathers Caleb and Christina in David’s airship to return to Chicago, and Nita helps them escape.