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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 and those allied with them are the enemy. Among the Abnegation wreckage, Dauntless leaders Max (Mekhi Phifer) and Eric (Jai Courtney) recover a box with all five faction symbols on its sides. 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.

17-year-old Divergent Tris (Shailene Woodley), her Divergent boyfriend Four (Theo James), her Erudite brother Caleb (Ansel Elgort), and Dauntless troublemaker Peter (Miles Teller) hide within the Amity compound. Eric leads a Dauntless crew to test all the occupants for Divergence. Peter gives up the group's location as the others escape and board a train headed into Factionless territory. Four reveals to the Factionless that his real name is Tobias Eaton, son of Factionless leader Evelyn (Naomi Watts), who Four still resents for leaving him with his abusive father, Marcus. At the Factionless hideout, Evelyn suggests an alliance of Dauntless and Factionless against Erudite, but Four declines. The next morning, the three leave for Candor, to meet up with the remaining Dauntless who were given shelter there, including Tori (Maggie Q) and Tris's best friend Christina (Zoë Kravitz). During the trek, a disheartened Caleb splits from the group. 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 a trial with the use of Candor's truth serum. The serum reveals the real events and they're absolved, but Tris tearfully admits killing Christina's lover Will, provoking her anger.

Candor is attacked by the Dauntless who have sided with Jeanine, and many are shot with metal disks. Tris is captured by Max and Eric who learn she has a Divergent reading of 100%, making her the perfect subject to open the box. Four shows up to save Tris, then executes Eric for his crimes. Meanwhile, Jeanine, frustrated that none of the Divergent subjects survived the simulations required to open the box, is approached by Peter, who suggests the best way to get to Tris is by exploiting her selfless Abnegation upbringing.

Back at the Factionless base, Four reluctantly agrees with Evelyn that war is inevitable. Jeanine activates the disks, which are a mind control device that causes Christina and her friends Marlene and Hector to robotically walk towards a ledge while asking for Tris's surrender. Tris and Tori manage to grab Christina and Hector in time, but Marlene plunges to her death. Overcome by guilt, Tris decides to turn herself in to Jeanine.

At the Erudite headquarters, Tris threatens to kill herself rather than comply, but is stopped by the presence of Caleb, who fully recommitted to Erudite. Tris agrees to undergo the trials provided that the suicides cease. Under Jeanine, Caleb and Peter's watch, Tris overcomes the first four simulations before requiring rest. The next day, after discovering Four was captured while trying to rescue her, she fails the Amity trial and her vital signs cease, to Jeanine's shock. Peter takes her body to Four, reveals he faked her death and assists Four in overpowering the guards. Tris is now determined to unveil the box's message, so with Peter's help they return to the simulation room and she successfully opens the box in front of everyone. A hologram explains that the walled city and the faction system were part of an experiment, with the Divergents as its ultimate goal; the world is waiting outside for them to rejoin it. Realizing she has lost all her power, Jeanine orders the box buried and Four and Tris executed. However, the Factionless break into the room, incapacitate Max and rescue Tris and Four. Jeanine and Caleb are arrested and the message is broadcast to the entire city. Hailed as a hero, Tris is eager to explore the outside world. In her cell, Jeanine wonders what might lie beyond the wall. Evelyn tells her she will never find out, then kills her.