The Purity War was, according to David in Allegiant, "A civil war, waged by those with damaged genes, against the government and everyone with pure genes." After the war was over, many demanded a solution to the problem; for this reason, the Bureau of Genetic Welfare was formed.
It was implied the Purity War was highly destructive, for it was said to have eliminated half the population of North America—"a level of destruction formerly unheard of on American soil".
It was also stated that the Purity Wars started with the use of conventional weapons, and later transitioned to biological weapons.
The Purity Wars were directly caused as a result of the genetic manipulation of the population (it is unknown if this engineering was exclusive to the United States or global). There was a small group of people who were opposed to this engineering and did not permit it to be done on themselves.
From what the Bureau of Genetic Welfare told the survivors from Chicago, the editing was to remove genes such as murder, crime, and other issues that plagued society.
Later, with an unclear interim period, the results of the engineering led to damaged genes rather than repaired ones. At some point, the people who were untouched took control of the American government and began to treat the people who were edited as damaged and second class citizens.
This caused discontent among the populations, which later resulted in a full scale conflict.
Little is known of the actual conflict itself, or the duration. The scale seemed to cover the entire United States. At the opening of the conflict the rebels used conventional weapons. Later, it transitioned to biological weapons. It is unclear if nuclear weapons were deployed.
Additionally, given the likelihood that this alteration was done globally, it is possible that there were other, linked conflicts. However, there is no information on what happened outside of the United States.
According to the Bureau of Genetic Welfare, the war caused unprecedented destruction, unseen on American soil. It can be presumed that the conflict was worse that the American Civil War, though it is possible that the Bureau was lying.
Much of the United States was heavily damaged and depopulated. Outside of Chicago, the surrounding suburbs were heavily damaged and abandoned either during the war or in the time after. The Bureau of Genetic Welfare was formed as a way to combat the genetic damage, and find a cure for it. From the set up of the compound, it appears that they also perform experiments in other areas such as agriculture, medicine, chemistry, and engineering.
David states that the west was 'wild country' and abandoned, that it was too hard to control the territory. The East was under strict government control, supplies were rationed, and the police were brutal unless a person was genetically pure.
Given that most of the history that Tris and her group were given was stated by the Bureau, or the rebel group devoted to destroying the Bureau, it is unclear how truthful the information provided was.