This post contains lots of spoilers!!
This book picks up right where Divergent left off - Tris, Tobias, Caleb, Marcus, and Peter are escaping to Amity. When they get there, the Amity agree to take them in but only if they live up to certain conditions - no fighting, no talking about the conflict, and they must work. They decide they can't stay there long.
While at Amity, Tris overhears Marcus talking to the Amity spokesperson about the attack. He tells her that Abnegation was attacked because of something that they know. They were going to make this information public, but Erudite attacked them to keep it secret. Tris is intrigued and tries to get this information out of Marcus, but he refuses to tell her. She tells Tobias about it, but he believes that Marcus is lying and that there is no information.
Erudite comes and attacks. Tris saves Peter from being shot. Tobias, Tris, and Caleb end up escaping without Peter and Marcus, who they assume have been killed. They end up being confronted by the factionless, who take them to their leader Evelyn, Tobias's mother. Tris is upset because she always believed that Tobias's mother was dead, but he apparently knew that she was alive. The factionless take them in for a bit. But then they decide to go to Candor, where the half of the Dauntless that are not teamed up with Erudite are.
The Candor make them undergo a truth serum test to make sure they're on the right side. Under it, Tris ends up saying that she shot Will, which understandably upsets Christina. Tobias is also upset that she didn't tell him. There are numerous fights between Tobias and Tris in this book that are basically along this same theme - they don't communicate well.
They reunite with the loyal half of the Dauntless. The Candor base is then attacked by Erudite/Dauntless and everyone is shot with a new simulation serum. The group is led by Eric and they are looking for those who the serum didn't work on - the Divergent. Tris discovers that Uriah is also Divergent. Eric plans on taking two of the Divergent back with him and killing the rest. Tris is able to stab Eric, not fatally, and a group of loyal Dauntless are able to overpower them and take control again.
Tori and Zeke (Uriah's brother) show up. They were suspected traitors but it turns out they were spies. Tori reveals that the Erudite have developed a new serum that will work over longer distances. Tris believes this is the serum that everyone was shot with during the attack.
Following the attack, the Candor decides to open talks with Erudite. They want the Candor to hand over the Divergent and a list of the people who didn't get the new simulation serum. The loyal Dauntless decide they need to elect new leaders and Tori and Tobias are among those chosen. They decide to leave Candor and execute Eric before they leave. They return to Dauntless headquarters.
Tobias and Tris get into another argument. He's upset because she's being needlessly reckless. She has a suicide wish. She also is still unable to hold a gun after she shot Will. But Tobias still asks her to come with him to a meeting with the factionless, where he agrees to team up with them to destroy Erudite and the faction system. Tris doesn't like it and they get into another fight.
One night the Erudite are able to control a few of the Dauntless to deliver a message - to turn over one Divergent or they'll take control of more every night. And then the 3 under control jump to their deaths. Tris is only able to save one of them - Lynn's younger brother. She is unable to save Marlene, who Uriah just started a relationship with. After this, Christina forgives Tris for killing Will because she saw how impossible the situation was and figures that it was probably similar with him.
Tris decides to turn herself in to the Erudite so that no one else will die. Tobias begs her not to go and she promises him that she won't, but of course she does anyway. At Erudite headquarters she's taken prisoner and experimented on. Jeanine is trying to develop a new serum that will work on Divergent. Tobias shows up - he's also been taken prisoner. She assumes it's because he came to die with her. He is able to get her alone and let her know that they are actually planning an attack and that she just has to hold on for a little while. Tris also discovers that her brother Caleb is on the side of the Erudite.
After being continually unable to find a simulation serum that works on her, Jeanine decides to execute Tris. It is, of course, while being executed that Tris finally decides she wants to live - that the best way to honor the deaths of her parents is not to join them but to live. Luckily, the serum that Peter injects her with is not the death serum, but one that only paralyzes her for a minute. Peter helps her and Tobias to escape. When she asks Peter why he would help her, he replies that she saved his life at Amity headquarters so he owes her.
They head to the Abnegation sector, where the factionless are. The Dauntless/factionless are planning to attack Erudite. Tris meets with Marcus, who reminds her of the importance of the secret information. This information will be destroyed in the attack, but he believes it needs to be made public. Tris agrees to help him, even though it means betraying Tobias.
Tris, Marcus, and Christina head to Amity, where they gather some allies - Johanna (Amity spokesperson), Cara (Will's sister - Erudite) and a few others. They head to Erudite. Once inside, they realize the information would be too important to keep on any computer and that it must be on the computer in Jeanine's lab. They make their way there but only Tris makes it in. There she discovers Tori about to kill Jeanine. Tris pleads with her not to, not until they've obtained the information, but Tori doesn't listen. That's when Tobias walks in and discovers that Tris has betrayed him. She confronts him about supposedly loving and trusting her but that he doesn't trust her judgment now.
Tris is taken downstairs and put with the Dauntless/Erudite traitors who have been captured. This is when she realizes that the factionless have all the weapons and that the loyal Dauntless have none. The factionless then announce that they will be starting a new society without factions. The Dauntless protest, but without their weapons, they are powerless.
Tobias comes back into the room and tells Tris that he shouldn't have doubted her - he found the information. A video starts playing on the screen - it is of a woman explaining how the factions started. Society had gotten so bad that they decided to shut away part of it to start over. When this new society had finally gotten things together, they were to help the outside world do the same. They should reveal themselves when there began to be a large number of flexible personalities - Divergent. The video ends with the woman taking on her new name in the society - Edith Prior (the same last name as Tris).