Nickie's great-grandfather has died, and the house where he lived, in a neighborhood called Greenhaven, is inherited by Crystal, who plans to sell it.

In Yonwood, there is a Prophet named Althea Tower who sees the future of the world in burning flames and smoke, and subsequently spends months in a dream-like semi conscious state, in which she mutters phrases and words.

Brenda becomes the power that directs the police in the town to enforce the 'war against evil' and slaps buzzing bracelets on offenders who don't comply.

The so called instructions gradually become more and more strict and unreasonable, beginning with things like no sinners, no singing, no lights, and eventually no dogs.

As with all books in the Ember series, there is an underlying crisis within the wider community, nation, or, in the case of The Prophet of Yonwood, world.

The tension between the US and the "Phalanx Nations" is a major contributing factor to the behavior and motivations of the characters, especially Mrs. Beeson and Hoyt McCoy.

Nickie is in the temporary care of her aunt, Crystal, and as with DuPrau's other lead characters, she develops a surrogate parental relationship in order to obtain support and guidance.