Insurgent picks up where Divergent left off, with Tris, Tobias, Caleb, Peter, and Marcus heading out of the city to Amity headquarters where some members of the broken-up Abnegation have gone for protection. Tris is taunted by nightmares of shooting Will, the friend that she killed while he was under the simulation. The Amity, led by representative Johanna Reyes, agree to shelter the refugees as long as they remain peaceful. Soon, however, Erudite and Dauntless traitors arrive at Amity to seek the refugees, and after a heated fight the refugees have no choice but to leave and escape back into the city. Marcus reveals to Tris that the reason Jeanine attacked in the first place was to steal some essential information that Abnegation had been trusted with to keep them from revealing it to the city. Tobias does not believe this, but Tris does.
On the train Tris and her friends encounter a group of factionless and head with them to the factionless headquarters in an old warehouse. Tris is astonished to find out that Evelyn, Tobias's mother, is leading the factionless, but Tobias has known she is alive for a while now. Evelyn and the factionless plan to usurp Erudite and create a society without factions, and Evelyn wants Tobias's help rallying the Dauntless to their cause. Tris and Tobias soon head to Candor headquarters, where the rest of the loyal Dauntless have taken shelter, but they are immediately arrested upon arrival.
The leader of Candor, Jack Kang, saw footage of Tris and Tobias in the Dauntless control room, supposed they were the ones running the simulation, and accused them of crimes against humanity. They face a trial immediately, and have to relay the details of what happened under the influence of Candor's famous truth serum. They are cleared of charges, but Tris reveals that she killed Will. This is the first time Tobias and Christina (Will's love interest) have heard of this, and Christina feels that Tris has betrayed her.
Traitor Dauntless invade Candor headquarters seeking people who are Divergent, led by Eric, a former Dauntless leader. They shoot needles into everyone's arms that inject them with a simulation transmitter so that they will be susceptible to simulations at all times. The traitor Dauntless capture Tris, but she takes a gun out of her back pocket and stabs Eric, severely injuring him. Loyal Dauntless stream into the room and drive the traitors off.
Tobias has been repeatedly called a coward because of the information he revealed under the truth serum, so one night at dinner he beats up his father, Marcus, to prove that he is not. Tris goes to Marcus afterward and reminds him that he could use her help in trying to get back the information that Erudite stole. Meanwhile, Jack Kang believes that having the Divergent in Candor puts them all in danger, and arranges a meeting with one of Jeanine's representatives to try and negotiate a deal to protect Candor.
Tris and a few of her friends go to eavesdrop this meeting, and realize that Jeanine is speaking through the Dauntless traitor she has sent to represent her using an earpiece. Tris knows Jeanine must be nearby; however, before she can figure out where she is, one of her friends, Lynn, shoots Max. A fight ensues, and Tris tries to go after Jeanine, but one of their friends is injured and they have to take her back to Candor. Tobias is angry at Tris for continuously risking her life so senselessly, and threatens to end their relationship.
They know that Jack will agree to Jeanine's demands to turn over all the Divergent, so they decide the best thing to do is return to Dauntless headquarters, where they will all be safer. They hold a Dauntless meeting and choose new leaders, ending up with Tori, a man named Harrison, and Tobias as leaders. They then execute Eric officially for crimes against Dauntless. Finally, they head back to the Dauntless compound, cover all the surveillance cameras with paint, and try to achieve some semblance of normalcy. Christina at last forgives Tris for killing Will.
Tobias takes Tris to meet Evelyn on a train, and they form an alliance between Dauntless and the factionless. Tris is not pleased with this, because she thinks Evelyn is using Tobias. Erudite soon strikes again with another simulation, making Dauntless members commit suicide every other night until one Divergent turns him or herself over for experimentation. Tris knows she has to stop this, so she lies to Tobias and Christina and turns herself in at Erudite headquarters, where Jeanine runs experiments on her to try and create a simulation that actually affects a Divergent mind. Tobias shows up there too, presumably to sacrifice himself and die along with Tris.
Jeanine reveals the secret weapon that has allowed her to manipulate Tris so effectively: Caleb, her brother. He betrayed Tris and their family in order to remain loyal to his faction, Erudite, and help Jeanine. The experiments continue, and Tobias finally reveals to Tris that he did not come here on a suicide mission, he came here to scope out headquarters and find Erudite's central control room so that when the factionless and Dauntless invade they will know where to target. He tells Tris to hold out for two more weeks, even though she now wants to die.
Tris continues to resist the simulations, and tells Jeanine that she will never be able to control her. Jeanine, angry, tells Tris that she will resume testing on Tobias instead, and schedules Tris's execution for the following morning. Peter, Tris's old enemy, leads her to her execution and appears to injects her with a death serum. However, this is not actually a death serum; Peter replaced it with one that merely causes paralysis, and sneaks her body out of the room so she can escape with Tobias. Peter did this because he could not stand to be in her debt.
They break out of Erudite and make it to Abnegation headquarters, where the factionless have camped out. They are about to begin their plan to bring down Erudite and abolish the factions, but Tris decides that it is more important that she help Marcus get this vital information from out of Erudite's hands before the factionless destroy everything. She enlists Christina's help, and they go to Johanna to try to get Amity on their side. When Amity refuses to get involved, Johanna breaks away from her faction because she knows stopping the violence in the city is the right thing to do.
Back in the city, Tris and the others head to Erudite headquarters to find the computer containing the stolen Abnegation information. The factionless have already begun their invasion. Tris and Marcus make it to Jeanine's private lab, where Tris fights a simulation in order to get past security. Once past, she finds Tori with a gun pointed at Jeanine, about to kill her. Tris knows she needs Jeanine to find the information on her computer and tries to stop Tori from shooting, but it is too late; she shoots, and Jeanine dies. Tori thinks Tris is a traitor, and sends her down to be tried with all the other traitors.
Tobias, however, finally believes that what Tris says is true, and forces Caleb to help disarm the security system on the computer so they can get the information. Just as Evelyn is talking about how there will no longer be any factions, Tobias comes down and plays the video that he has retrieved. It is a woman speaking about how the factions were created as an experiment in order to get rid of the flaws in human nature and create Divergent people with flexible, virtuous minds. Lastly, she reveals that she will be joining the society, too, voluntarily forgetting everything and taking the name Edith Prior.