Randy Bragg, the protagonist, is a man who dabbles at law and lives a life with little purpose. This changes when his brother, Colonel Mark Bragg, sends him a telegram with the code words "Alas, Babylon"-their private code for disaster. Mark, who is on the staff of the Strategic Air Command, believes World War III between the United States and the Soviet Union is about to begin. He sends his wife, Helen Bragg, and his children, Ben and Peyton, to stay with Randy in Fort Repose, Florida.
The day that Helen and the family arrive, a U.S. Navy fighter fires a missile at a Soviet reconnaissance aircraft. The missile misses and hits an ammunition dump at Latakia, Syria.
Early the following morning, Mark is on duty at SAC headquarters in Omaha, Nebraska. He suspects an attack is imminent. He recommends that SAC ask for the authority to use nuclear weapons. Ninety-five seconds later, American radar reports an attack underway. "Thanks for the ninety-five seconds," the SAC commander says to him.
The effects of the war on Fort Repose are indirect. Northern tourists are trapped in their motels. The local bank manager tries to get instructions from Jacksonville as Jacksonville is destroyed. The local disc jockey nervously reads instructions on the CONELRAD system.
As the effects of the disintegration of outside society get worse, Randy finds himself growing stronger. He organizes his neighbors to provide housing, food, and water for everyone. He organizes the community into self-defense, guides his family, and helps find salt and new supplies of food when they grow short. He fights "highwaymen" who rob travelers, including the local doctor. With the struggle for survival, the institution of segregation vanishes. Some in Fort Repose discover faith; others degenerate into drunkenness. Peyton and Ben adapt to the need to guard food supplies and to do without irreplaceable resources.
When the Air Force makes contact with Fort Repose again, the community has survived, but at a cost.