After Edith Prior's video footage reveals to the city that there is a whole world outside of the city limits, the city's social system is in shambles. The factions have disintegrated, and Evelyn rules the city as a tyrant with her factionless army. Tris, Tobias, and their friends set out on a mission to discover what is outside the city. Their escape plan is one of two missions of a rebel group known as the Allegiant, who also wish to reinstate the faction system.
Outside the city, the group finds themselves at the Bureau of Genetic Welfare, a government agency supposedly working to fix the genetic damage that has been a problem in the United States for many years. The Bureau's leader, David, tells Tris and Tobias that Chicago (their city) was merely one of many experiments aimed to cure this problem of genetic damage. They are told that the term Divergent simply means that someone possesses cured genes, and they realize that their entire livelihood has been nothing but a lie.
As the group from the city tries to cope with these discoveries, a girl named Nita informs them of the evils of the Bureau -- treating genetically damaged people as second-rate citizens, creating the simulation serum that led to the killing of most of the Abnegation, lying constantly... Nita enacts a plan to undermine the authority of the Bureau, but Tris ends up thwarting this plan when she realizes that Nita is planning an assassination of Bureau leaders.
Tris and Tobias must come to terms with life outside the city, while deciding for themselves if the Bureau is an evil organization. Eventually, when the city is on the verge of an all-out war between Evelyn and the Allegiant, Tris and her friends must act to stop the Bureau from resetting the memories of everyone in the experiment.