In the house on the River Road, Randy, Helen, thirteen-year-old Ben Franklin, and eleven-year-old Peyton are awakened by what feels like an earthquake. The earthquake turns out to be twin nuclear explosions, far south of them, in Miami and at the SAC base in Homestead. Clustered together outside the house, they see fighter jets soar overhead, and then a third nuclear explosion occurs, to the southwest, in the direction of Tampa-St. Petersburg. Peyton, who happens to be looking right at the explosion, is blinded by the burst of light.
Randy hurries into town, looking for Dan Gunn. He passes a crashed car and a woman's dead body on the way, and finds Fort Repose in turmoil, with people crowding the stores and the gas station. The guests in the local hotel are milling about in confusion, and Randy finds Dan Gunn in one of the hotel rooms, seeing to a heart attack victim. Dan, hearing what happened to Peyton, says that she will probably be all right, and prescribes some eye drops and says that she should rest in a dark room. Randy hurries back to the river road, passing a gang of escaped convicts carrying guns, and a car carrying Florence and Alice.
Florence makes her way to the telegraph office, where she deals with a long line of people trying to send messages, most of which cannot be sent, since communication north of Jacksonville is forbidden. Edgar Quisenberry, the bank president, comes in, and tries to wire to Jacksonville to ask for instructions from the Federal Reserve Bank there. However, as his message goes through, Jacksonville is wiped out by a nuclear weapon. Quisenberry returns to the bank, where a huge crowd shows up, wanting to withdraw money. After a time, the demand grows so great that he is forced to close the bank. He makes his way home, distraught by the collapse of the financial system. Unable to bear the idea of a world in which banks and money have ceased to exist, he shoots himself.
Forever afterward, the first day of nuclear war would be known simply as "the Day" in Fort Repose. For Randy, listening to the radio in his home, the events seem difficult to understand, especially when the new "Acting President" of the United States comes on the radio. Washington has been destroyed, and with it, the President and the government have gone. The United States is now led by Mrs. Josephine Vanbruuker-Brown, formerly the Secretary of Health, Education and Welfare. In a speech, she reports that many major cities have been wiped out, but "that our reprisal was swift, and, from the reports that have reached this command post, effective." Later that night, Dan Gunn shows up to look at Peyton, who has been wearing a bandage over her eyes. When it is removed, her sight has begun to return. Dan has a drink with Randy, telling him that several people have already died or committed suicide, among them Edgar Quisenberry. Then the two men discuss the possibility of radiation poisoning. Fortunately, the prevailing winds have been blowing east, carrying the fallout toward the Atlantic Ocean.
After Dan leaves, Randy visits his neighbor, Admiral Hazzard, a retired Navy officer. The Admiral owns a ham radio, and he has been monitoring signals during The Day, and trying to piece together the military situation. As he and Randy talk, Orlando, to the southeast, is hit with a missile, and the lights go out in Fort Repose.
Alas, Babylon is largely a cautionary tale, and the immediate aftermath of the nuclear explosions is meant to demonstrate that the United States is completely unprepared for a nuclear attack. In Washington, the President, Cabinet, and Congress do not even have time to escape before the bombs fall. As a result, the government is turned over to a low-level Cabinet Secretary. Meanwhile, civil order breaks down in Fort Repose almost immediately. There are accidents and dead bodies on the highway, escaped prisoners wandering around with guns, and mobs in the stores and gas stations. There is no one to restore order; once communication with the outside world is cut off, no one is willing to take responsibility for the situation in the town.
The novel also explores how individuals react to such a sudden shift in the way the world works. Randy rises to the occasion, remaining calm and planning what is best for the family. Likewise, Dan throws himself into his medical work to try to take control of the situation. The older women, Florence and Alice, acquit themselves, bravely making their way into work and carrying on with their jobs and lives despite the crisis. Their courage and their refusal to crack under the pressure is contrasted with the behavior of Edgar Quisenberry, who holds the bank together in the afternoon, but finally breaks down and kills himself when he realizes that money has suddenly become worthless. Dan delivers his epitaph: "Some people melt in the heat of crisis and come apart like fat in the pan. Others meet the challenge and harden."
The Day begins and ends with nuclear explosions. The last one, incinerating Orlando, knocks out power in the town. "The lights went out," Frank writes, "and in that moment, civilization in Fort Repose retreated a hundred years." The image of darkness falling is a motif that recurs at the novel's close. It points to the extinguishing of the modern world, and the plunge into barbarism.