Soon after they do have to run ,but for reasons they didn't expect. Some of the traitor Dauntless were sent to find the group and bring them to Erudite Headquarters by Jeanine Mathews, Erudite's leader. When someone almost shoots Peter during the fight Tris pushes him out of the way without looking on instinct. After she feels like she could almost kick herself but little did she know help her later. Surprisingly everyone made it out alive but they went separate ways. Peter was captured by Erudite then was forced to help them capture Tris and Four. Marcus went to what was left of the Abnegation sector of the city then to Candor. Tris, Four, Caleb, and Susan go run on a train that is controlled by Factionless. They are kept alive because Tris had helped Edward, who is now Factionless, when he was stabbed by Peter in the eye in the first book and because of Four's true identity, Tobias Eaton the son of Evelyn Eaton and Marcus Eaton.
Everyone thought that Evelyn had died of the birth of her second child who died stillbirth, but that was far from the truth. She was never pregnant with a child. She was kicked out by Marcus. She left Tobias because she thought he'd be better of with Marcus in Abnegation than with her in Factionless. Soon she became leader over the Factionless and one of the only Abnegation to ever go become Factionless. She has been looking for Tobias ever since she heard about him surviving the Erudite, Dauntless attack on Abnegation. She wants him to convince the Dauntless to work with the Factionless to take down Erudite.
Tris, Four, Caleb, and Susan are brought to Factionless to talk to Evelyn. Tris immediately dislikes Evelyn because of what she did to Four. Four, to, is still mad Evelyn because he doesn't know her whole story. Evelyn doesn't like Tris either and tells her that she is family and is permanent while Tris is just a girl who Tobias will get tired of and get rid of. Tris really doesn't like her then but keeps it to herself for Tobias. Soon after they leave to Candor because that's where the Loyal Dauntless were. When they get there they are put in custody and are told that they must undergo trial after injected with piece serum. Christina and Uriah tell them that it'll be alright. Christina walks Tris to the trial even though she knew that she probably shouldn't. Tobias went first. They started by asking what they thought were little questions but to Tobias they weren't. They asked him what his real name was, who his parents were, why he transferred to dauntless, and why he stayed. His first 3 answers shocked everyone other than Tris. The last one shocked everyone including Tris, she didn't know that she was the reason he stayed. They finish their questions from his side of the story then call Tris up. After the first couple of questions she breaks out of the phase of the serum and realizes that she can fight the serum off. She still answers the questions truthfully until it gets to a question about her secret. She thinks about lying, the only reason she didn't was because she didn't want to. She wanted to just let out her secret that she has been keeping from everyone including Tobias. She killed Will.
When she says it Christina, Tobias, and everyone is shocked. She tries to talk to Christina but Christina simply ignores her, blinded once again by her own heart break. She walks outside avoiding Tobias because of fear of what he will say. Uriah notices ,like he did in Divergent, that she is sad and invites her to go do something fun with him, Lynn, and Marlene. While on their way out the door an attack from the Traitor Dauntless starts. Tris then finds out Uriah is Divergent because everyone was injected with a serum that was activated by a gas that was thrown in the room. Tris and Uriah split up to try to find and help people but they both where captured. While in the elevator with Eric they witness how cold blooded he really is when he kills a 10 year old Candor boy. When Eric gets near Tris again she stabs the foot she shot during the war in Abnegation in her first attempt to escape.
The loyal Dauntless hear his scream of agony and rush into the room just in time to save Tris and everyone else in the elevator. Eric was locked up and Zeke, Uriah's brother and Tobias' best friend, and Tori, Tris' test administer, come back from their spying in Erudite. Since all of Dauntless' leaders are dead or part of the Traitor Dauntless they vote for leaders. They voted for Tris, Tobias, Harrison, and Tori. Since tin the rules the Dauntless have states that they are to have an odd number of leaders Tris volunteers to go out. She knows that Four wants the position and exactly why he wants it and even though she doesn't agree to it, she doesn't want anymore problems with him. After they are done they hear an announcement that says that the Candor are making a deal with the Erudite. For their safety they have to give up Eric unharmed, tell the number and names of people that didn't get shot with the serum, and the number and names of the Divergent. The Dauntless make a run to their headquarters and kill Eric so that the Candor can't ally with Erudite. Once they get their they paint ball all the cameras. Or so they thought. They missed one camera in the initiates old dormitory that caused the death of Marlene. The Erudite watched that camera and saw that Marlene, Hector, and another girl had been shot with their serum. They then activated it and caused them to jump the chasm and relay a message to the Divergent. "I have a message for the Divergent. This is not a negotiation. It is a warning. Every two days until one of you delivers yourself to Erudite headquarters, this will happen again."
Tris decides that this will not happen again. She goes tot he Erudite headquarters the next morning even after telling Tobias that she wouldn't go. She is then put in a room where she stays for approximately a couple of weeks when she is not being tested. While she is there she negotiates with Jeanine Matthews. "If I cooperate, I get to see the scans." At first Jeanine tried to argue but she failed seeing as she needed the knowledge so that she could make a serum that works on Divergent. While she is there Tobias comes but not for a suicide mission. He comes to tell Tris to hold on because a plan to save her is in action. She is a week away from when the day of her execution is when they moved it up. No one expected it so they weren't ready to save her because they didn't know. Tris goes to the execution room and is injected with a serum meant to kill her but it doesn't.
Peter had changed the death serum to a non-permanent paralytic serum and dyed it purple. Then he had help from other Erudite to make the heart monitor stop working. He then wheeled her out and to the room Tobias was in. When Tobias came out he was upset but then Peter assured him she was fine. Then Tobias grabbed Peters gun and Peter grabbed Tris and they ran to the incinerator that was turned off for the day and slid outside. They ran to an abandoned building and stayed there for a couple of hours before making their way to the Abnegation sector where all the Factionless and Dauntless who aren't weird for simulations are. Once they got there and Tris rested she went for a walk were she saw Marcus and told him she would help him get the information about outside the fence from Jeanine. To do this Tris has to lie to Tobias again but this time it's worse since she's working with his father ,who he despises, against him.
While Four and his mom are getting people ready for the invasion of Erudite Tris is working with Christina and Marcus to get ready to save the information. Before the Dauntless and Factionless group go out her, Christina, Marcus, and the small group they made go to Erudite dressed in blue, the Erudite faction color. When Tris almost has the information from Jeanine it is token away by Tori when she killed Jeanine before she got the information. While Jeanine dies Tris is took to the basement cell by Uriah. She feels not only regret but also loss because Tobias won't even look at her. She knows she screwed up as she sits in the cell with Christina. Tobias comes into the room and grabs Caleb which makes her confused but she passes it of as the Factionless and Dauntless trying to erase all the information that the Erudite has. Evelyn starts her speech about how the factions will be disbanded and everyone will be like the Factionless and also how the traitors will be put under trial and the people who helped her would be rewarded. While this is going on Tobias comes back in the room just as the information she was searching for comes on.