Tris, Tobias, and a small group of others that have aligned themselves with the Allegiant--those who are opposing Evelyn's "factionless" dictatorship--have left the confines of Chicago and made their way to the Bureau of Genetic Welfare. They are told:
"A few centuries ago, the government of this country became interested in enforcing certain desirable behaviors in its citizens. There had been studies that indicated that violent tendencies could be partially traced to a person's genes--a gene called 'the murder gene' was the first of these, but there were quite a few more, genetic predispositions toward cowardice, dishonesty, low intelligence--all the qualities, in other words, that ultimately contribute to a broken society." (121)
People who consented to be a part of the "genetic manipulation experiment" "were given the option to give a gift to [their] future generations, a genetic alteration that would make their descendents just a little bit better" (122). Unfortunately,
"[W]hen the genetic manipulations began to take effect, the alterations had disastrous consequences. As it turns out, the attempt had not resulted in corrected genes, but in damaged ones," David says. "Take away someone's fear, or low intelligence, or dishonesty . . . and you take away their compassion. Take away someone's aggression and you take away their motivation, or their ability to assert themselves. Take away their selfishness and you take away their self-preservation. If you think about it, I'm sure you know exactly what I mean." (123)
Thank you! This is exactly what I have been thinking about the factions all along! I just couldn't understand how people could read the books and be all, "ZOMG, what faction would YOU be in?" NONE! The whole system is based on a terrible premise! Garr, smash! Well, I didn't take it that far, but you know what I mean.
So the effects of these genetic manipulations lead to "the Purity War. A civil war, waged by those with damaged genes, against the government and everyone with pure genes. The Purity War caused a level of destruction formerly unheard of on American soil, eliminating almost half of the country's population" (123).
After the war is over, people who are "genetically damaged" are placed in "secure environments" based in various cities. The Future Chicago we become acquainted with the in the first two books is just one of these experiments, and it is considered one of the most successful. Although Edith Prior's speech in the video is a somewhat fictionalized version of the city's purpose, the goal of creating an abundance of Divergent people is true, as Divergence is a sign of being genetically healed--or returned to a state of Genetic Purity. (What is unclear to me is why the faction system in Chicago is deemed to have been helpful, as I would think that it would merely encourage people to become more entrenched in their GMO-induced traits. Wouldn't it make more sense to actively encourage intermingling, in order to cultivate Divergence?)
Anyway, it doesn't take too long to find that the Bureau of Genetic Welfare--where Tris, Tobias, and the others have been taken in--isn't quite as beneficent as it appears at first glance. After genetic testing shows that while Tris is Divergent, Tobias is actually not (he only displays certain Divergent characteristics), we learn that there is a caste system that divides GP (genetically pure) from GD (genetically damaged). The GDs are pitied but also treated as inferior, expendable, and not capable of being held responsible for their actions.
Tobias, as a "GD," is pulled into a plot orchestrated by a group of GDs. As far as he knows, their aim is to break into the Weapons Lab and steal the memory serum--something that has been used to reset the memories of certain people in the experiments--for example, Amanda Ritter as she was about to become Edith Prior, or people who found their way out of the gates of the city and caught too much of a glimpse of what lies beyond. In truth, the aim is to release a death serum in a series of targeted attacks. Tris manages to leap in and prevent the operation from being completed.
Nevertheless, Tris agrees that the GP/GD divide is harmful and misguided, and she and Tobias become a part of a more sane group dedicated to addressing it. While they work on those plans, they become aware of an alarming situation. Chicago is poised to go to war: Evelyn's factionless vs. the Allegiant, co-led by Johanna and Marcus. In order to rescue their experiment, the Bureau plans to unleash the memory serum and reset everyone's memories. Apparently, this was done there a few generations ago (see the destruction in the factionless sector) and is a regular tactic whenever an experiment is on the verge of failing. Our heroes cannot allow that to happen to their families and the community they came from.