Indianapolis was one of the experimental cities run by the Bureau of Genetic Welfare. In Allegiant, Nita states that she was from Indianapolis. She also says that the Indianapolis experiment failed because no factions were formed from the start. In that experiment they only used a series of strict guidelines like no fighting, curfew, etc. But a rebellious group of many people made a bomb, and had blown it up in a government building.
It is revealed in Allegiant that Chicago is an experiment city run by the Bureau of Genetic Welfare, and is one of several cities run by the group, under the United States Government. Most have failed or been shut down, including Indianapolis. Other cities mentioned without a fate being revealed include Detroit, Saint Louis, and Minneapolis. The only government controlled cities mentioned is Milwaukee.
Nita was from the city, but was taken to the Bureau of Genetic Welfare after an insurrection broke out.