Plot

Five days after the assault on the Abnegation faction by Erudite leader Jeanine (Kate Winslet) and her mind-controlled Dauntless soldiers, Jeanine has declared martial law and that the Divergents - those with the qualities of multiple factions - and those allied with them are the enemy. Among the Abnegation wreckage, Dauntless leader Eric (Jai Courtney) and his platoon recover a five-sided box: each side has a faction symbol. Jeanine presumes it contains data from the city's founders and the means to end the Divergence problem. As only a Divergent is capable of opening the box, she orders the capture of all Divergents.

Tris (Shailene Woodley), Four (Theo James), Peter (Miles Teller), and Caleb (Ansel Elgort) hide within the Amity compound. Soon after, Eric and his fleet arrive to test all the occupants for Divergence. Peter gives up the group's location as Tris, Four, and Caleb escape and board a train headed into Factionless territory. After fights with the Factionless aboard, Four reveals his name-Tobias Eaton-which prompts the Factionless to stand down and reply that they have been searching for him.

Four, Tris and Caleb are given amnesty at Factionless. There, Tris and Caleb discover that the Factionless leader is Four's mother, Evelyn (Naomi Watts). She suggests that Dauntless and Factionless should ally against Erudite, but Four declines. The next morning, the three leave Factionless for Candor to meet up with the remaining Dauntless; during the trek, Caleb tells his sister Tris that he cannot continue with them and goes in a different direction. Upon arrival, Tris and Four are arrested and brought before Candor leader Jack Kang (Daniel Dae Kim), who intends to deliver them to Jeanine. However, Four pleads for Jack to conduct a trial in Candor with the use of truth serum. During the trial, Four communicates his motives and is absolved. Tris tearfully admits her guilt in shooting and killing Will, which angers Christina.

Candor is attacked by the Dauntless who have sided with Eric, and many people are shot with pellets of new simulation serum. Tris is captured by Eric who learns she has a Divergence reading of 100%, making her the perfect subject to open the box. Eric arrests Tris, but Four and the Factionless allies arrive to save her. After a brief exchange, Four shoots Eric in the head for the murder of hundreds of people. Back at Erudite, Jeanine, frustrated that none of the Divergent subjects have survived the simulation trials required to open the box, is approached by Peter, who pledges his loyalty to Erudite, and suggests the best way to get Tris to surrender is by exploiting her humanity.

Back at the Factionless base, Four reluctantly agrees with Evelyn that war is inevitable and that they need to prepare. Jeanine activates the pellets, causing Christina, Marlene and Hector to repeatedly chant that Tris must turn herself in or more death will follow, as they step closer and closer to the edge of a tall structure. Tris and Tori then climb the sides of the roof as Tris rescues Christina and Tori, Hector. However, Marlene plunges to her death. Overcome by guilt, Tris decides to turn herself in. That night, she and Four sleep together, and then she quietly slips away.

Upon arrival at the Erudite headquarters, Tris is immediately arrested. She agrees to undergo the trials provided that the suicides cease. Tris overcomes four of the trials, however, when her vitals drop, Jeanine reluctantly halts the simulation so that Tris can rest. Peter realizes that in one of the sims, Tris spares Peter's life, even though he sold her out to Jeanine. He decides to change his loyalty to Tris.

Tris then discovers that they have captured Four. She fails the final trial and her vital signs cease. Her body is wheeled over to Four's cell so the latter can mourn, but when she awakens, Peter assists Four in overpowering the guards, revealing that he had faked her death by injecting her with a sleep serum. Tris is determined to open the box and find the truth about its message; she and Four head to the simulation room, while Peter returns to the control room to secretly grant them security access.

Overcoming the final trial, Tris successfully opens the box. A woman explains that the walled city and faction system is actually an experiment they devised, that the Divergents are actually the success of the experiment, and that the world is waiting outside for them to return to humanity. Realizing she has lost all her power, Jeanine orders that the box be buried and that Four and Tris be executed. However, the Factionless army breaks into the simulation room to rescue Tris and Four. Jeanine and Caleb are arrested. The message from the box is broadcast to the entire city. Tris is hailed as a hero by the masses, eager to explore the world beyond the wall. As Jeanine looks out from her cell, she states that after 200 years since the city was enclosed, there is no telling what awaits them beyond it. Evelyn tells her that she will never find out and kills her.