Jeanine Matthews (Kate Winslet) sends a message to every faction in the city. She says that after the war, peace seemed unattainable. Now, she feels the opposite way, and that peace can be achieved so long as they purge the city of their one enemy - the Divergents. At the same time, Jeanine's men go to the Prior home in Abnegation and retrieve a box with a symbol of each faction on it, holding what is believed to be a message from the founders of the city. They need a Divergent to unlock it.
Tris Prior (Shailene Woodley) runs back to her home in Amity with her brother Caleb (Ansel Elgort) and lover Four (Theo James). She approaches the residents of Amity, but they all stand away from her. Tris sees her parents Andrew (Tony Goldwyn) and Natalie (Ashley Judd) bloodied, and Natalie says that Tris killed her and all of the people around her. This is only a nightmare. In reality, Tris is adjusting to Amity with Caleb, Four, Peter (Miles Teller), and Four's father Marcus (Ray Stevenson). Four remains distant from Marcus, despite how much he wants to talk to his son.
During lunch, Tris talks about wanting to go back to Erudite and kill Jeanine to prevent more deaths from happening. Caleb argues that this is a bad idea. Peter makes a comment on not getting Caleb killed, just like how Tris got her parents killed. Enraged, Tris attacks Peter with a knife, cutting his cheek. The leader of Amity, Johanna Reyes (Octavia Spencer) calls Tris to her office, saying that her presence in what is supposed to be a peaceful community is distracting and that they may be asked to leave. Johanna warns Tris not to let her want for revenge get ahold of her. Then, a team of vans, led by Eric (Jai Courtney) and Max (Mekhi Phifer), comes bursting through the gates, hunting for Divergents. Tris, Four, and Caleb hide in the office, but Peter rats them out, forcing them to make a run for it. The soldiers aim their guns at them, and Marcus stands in their way, leading to him getting knocked out as Four watches. The three evade the soldiers and make it down to the traintracks. Four holds the soldiers off and just manages to jump over the tracks before the train hits him.
The three hop the train and encounter a large group of Factionless people led by Edgar (Jonny Weston). They violently attack the three after Edgar almost pushes Caleb off the train. In self-defense, Caleb ends up beating one Factionless to death, horrifying him. They stop attacking when Four says his name is Tobias Eaton. Knowing who he is, the Factionless take the three to their leader and Four's mother, Evelyn (Naomi Watts). She explains that she faked her death when Four was six because Marcus was too abusive, but she regrets leaving her son behind. Her plan is to unite the Factionless and Dauntless to fight back against Jeanine and her forces. Four refuses to have any part in his mother's plans.
That night, Tris is sleeping with Four, when Evelyn appears in the doorway. She sits by the bed and asks Tris if she thinks he will still love her when he realizes what she really is - deadly. Tris then sees Four bloodied by her side. It's another nightmare.
The next morning, Tris and Four head to Candor, but Caleb heads in another direction. In Candor, Tris and Four reunite with the surviving Dauntless, including Christina (Zoe Kravitz) and Tori (Maggie Q). Christina asks Tris if she's heard from their friend Will, unaware that Tris had to kill him in his hypnotic state. Tris says she hasn't heard anything. Tris and Four are then apprehended and brought before the Candor leader Jack Kang (Daniel Dae Kim). He doesn't believe that they are truthful in what they say about Jeanine issuing the attacks and then framing them for crimes she committed. Four convinces Jack to let the two of them stand trial.
Four is injected with a truth serum and stands before the Candors. He tells them how he joined Dauntless to escape his father's abuse and that he planned to join the Factionless until he fell in love with Tris. Tris goes up with the serum in her, but the more she resists telling the truth, the more it pains her. She then admits that she was responsible for the deaths of many, including her parents and Will, to the shock and anger of Christina.
Back in Erudite, Jeanine is testing Divergents out to see who can unlock the box. She has a girl put in a simulation, but the girl dies. Jeanine determines that a particularly special Divergent must be brought to complete the task. Peter comes in and swears loyalty to Erudite. He tells Jeanine the best way to get Tris to give herself up is to play to her humanity.
Tris stands on a rooftop where she is approached by a young man named Uriah (Keiynan Lonsdale). He engages in pleasant conversation with Tris when Eric and his soldiers invade and start shooting the Candors with a sim serum to the neck. He has people lined up and starts to scan them to see which Divergent it is that they need. Eric scans Uriah and sees he is 10% Divergent, and he executes him. Eric then scans a little girl who is 40% Divergent. Before he can shoot her, Tris pushes him over. Max comes over to scan Tris and sees she is 100% Divergent. Four shows up and fights Eric, bringing him to his knees with a gun to his head. Eric asks if Four can live with killing someone the way Eric already has. Four shoots him in the head.
The sim serums activate on Christina, a young boy, and a girl named Marlene (Suki Waterhouse) as they stand over a ledge. They chant in unison for Tris to turn herself in or more will die. The three of them move closer as Tris and Tori run to rescue them. Tris grabs Christina and Tori grabs the boy, but Marlene falls over to her death.
Four returns to Factionless to join his mother's cause against Erudite. A guilt-ridden Tris decides that she must turn herself in to Jeanine if she wants to prevent anymore deaths. Once she gets to Erudite, she is immediately taken in and brought to the sim room.
Caleb, having rejoined Erudite, meets Tris in the sim room before it commences. He claims it is selfless of him to allow his sister to risk herself for the good of many. Tris is stuck with multiple wires and must go through a simulation of every faction to unlock the box. Her first test is a Dauntless sim. She is in the ruins of the city where she sees her mother in a building. The building catches fire, and Natalie calls Tris for help. Tris runs to her as the building starts to float into the air. She grabs a pipe and climbs to the top. She falls off briefly but manages to catch up and climb into the home to grab onto her mother. After she passes this, she must go through the Candor sim, which involves a sim of Four breaking her out with others behind him. Tris gets a gun and faces Peter on the floor. She spares his life and keeps going. She then realizes that Four isn't real, and she passes the sim. She also passed the Abnegation sim by sparing Peter's life. Tris starts to lose energy, and Jeanine reluctantly allows her to rest up before continuing.
When the tests continue, Tris is put in the Erudite sim, which puts her in a building as it explodes. She flies and falls back several hundred feet and smashes into the ground. This causes her to appear dead, to Jeanine's frustration. Peter brings Tris's motionless body to Four, who reacts angrily toward Peter. Tris then gasps a breath of air, and Peter leads Four to attack the guards, now helping the heroes out.
Peter gets into the computer system and lets Tris complete the final sim, Amity. She is forced to fight herself, as she is the one person she hates more than Jeanine. Sim-Tris taunts Real Tris over the deaths of her loved ones, but Real Tris knows she will eventually be able to forgive herself. After she passes this, the box is unlocked. Everyone sees what the message is - a woman (Janet McTeer) says that everyone in the city was part of an experiment to see if humanity can continue to thrive, and that the true saviors of this world would be the Divergents, so if one were to unlock this message, it would mean everyone is ready to go beyond the walls of the city. Knowing this would eliminate her power, Jeanine orders the box to be hidden from everyone, and for Tris and Four to be executed. The Factionless army then invades, seizing Jeanine and the box.
The message is played throughout all the factions. Everybody starts heading toward the walls and outside the city. Tris is seen as a hero for leading them to a new discovery. Meanwhile, Jeanine watches from the window in her cell as everybody advances beyond the city. Evelyn comes in behind her. Jeanine says that after 200 years since the city came to be, she wonders what could be out there. Evelyn tells her she'll never find out, and she ends Jeanine with a bullet to the back of the head.
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