The story starts off with a young girl named Nickie who is traveling with her Aunt Crystal to an old house in Yonwood, North Carolina. 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. Over time, Nickie begins to love the house and finds a girl named Amanda who lives there. She is there because she used to look after Arthur Green, the great grandfather of Nickie. Plus, Amanda has a dog named Otis that she gives to Nickie. 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. A woman in the town calls them insructions from God and requires townspeople to comply with her interpretation of the words, and insists that the entire city quit their "wrong" ways and start to be good people, so God would be with them. She 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. During the time, verbal conflict between the U.S. and the Phalanx Nations is going on. The U.S. fears that the Phalanx Nations are trying to send terrorist spies to the U.S. and they take immediate action, although the U.S. never really goes to war with them until 50 years later. Nickie meets a boy named Grover who is obsessed with snakes, but has to give them away because Ms. Beeson says that they are sinful. There is also an old, grumpy man named Hoyt McCoy, who is mean. However, he ends up being a kind man; he studies the stars and made contact with aliens. Hoyt McCoy went to Washington and stopped the war. In the end of the book, Nickie writes a journal that she hides behind a rock for someone to read later in the future. In The City of Ember, Lina Mayfleet and Doon Harrow find the journal when they are escaping/leaving Ember, and in The Diamond of Darkhold, a satellite sent out by Hoyt and other scientists is sent off into space, which later returns to Earth from an Alien planet.

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