Dr. Kerans stands on the balcony of the Ritz Hotel and watches the sun, which is an ellipse, rise. It's already hot and he's spent the morning dawdling instead of working. He wonders if he should contact his commander, Colonel Riggs, but remembers that his radio's battery is dead. Finally, Kerans hears Riggs approaching. He dresses and runs down to the dock where Riggs invites himself up for a drink. As they drink, Riggs tells Kerans that the unit has received a command to move north to Camp Byrd permanently. Kerans is shocked. Riggs asks for help convincing Beatrice to leave the city and asks Kerans how he's been sleeping. Kerans says he slept fine.
As Kerans and Riggs float through the lagoons that cover the city, Kerans watches the giant iguanas in the windows. Kerans is uninterested in the contents or the history of the cities. His fellow biologist, Dr. Bodkin, is old enough to remember living in the cities. Seventy years before the present, solar storms damaged the earth's atmosphere, leaving is vulnerable to solar radiation. The planet warmed rapidly, and plants and animals mutated due to the radiation. Bodies of water expanded as the ice caps and glaciers melted, entirely altering the landscape of the globe. Now, people only inhabit the Arctic and Antarctic circles. Kerans and Riggs take the elevator up to Beatrice's top floor apartment, where she's lounging by the pool. She brushes off Riggs and Kerans's attempts to convince her to leave. When Riggs leaves, Kerans remains for the afternoon. He studies paintings by Delvaux and Max Ernst and tells Beatrice that if they stay, they stay for good.
Later, Kerans returns to the base and sneaks into the armory. He studies the weapons and explosive gas but steals only a broken compass. He leaves the armory for the sick bay, where Dr. Bodkin and the bedridden Lieutenant Hardman are in a private room. Bodkin is running a heater and Hardman is listening to drumming on a set of headphones. Finally, Bodkin stops the record player and turns the heater off. He tells Hardman how to operate a set of alarm clocks and Hardman insists that he has begun dreaming even when he’s awake. Kerans lets slip that they're leaving in three days, which makes him feel like he's losing control of his motives. Kerans and Bodkin paddle to the testing station. In their lab, the doctors sit and Bodkin explains his theory of neuronics to Kerans: that the entire world, humans included, are following a backwards journey, and the terrifying dreams that many are now experiencing are actually ancient biological memories that mean a person is moving backwards in evolutionary time. Kerans thinks it's a valid theory. He pulls out the compass and thinks about the idea of "south."
Lieutenant Hardman disappears the next day. Kerans acts as though he's going to leave with Riggs, though he hasn't fully decided what he’ll do. He goes to see Beatrice first thing and finds her in her very hot apartment. He fixes her air conditioner and tries to make her pour her drink out, but she insists she needs the drink after dreaming. Riggs’s helicopter arrives and signals to Kerans that Hardman escaped. Kerans boards the helicopter and joins the search team, and eventually tells Daley, the pilot, that they should look south. Riggs agrees, and Kerans spots footprints leading to an apartment building in a southern lagoon. The men search the building, where Kerans stumbles upon Hardman. Hardman jumps out the window and tries to move his makeshift raft back into the water and seems unaware that he's surrounded. When he finally realizes he is surrounded, he shoots Wilson, one of his orderlies. The group follows Hardman to a town square above the water level, where Riggs allows Hardman to escape south.
That night, Kerans has his first dream: the sun makes a drumming sound, and the lagoon is filled with snakes and eels. Giant lizards roar at the sun, and Kerans feels like he's part of the lagoon. When he wakes, he finds Bodkin in the testing station gallery. Bodkin explains that about half the men experience the dreams. Riggs arrives to discuss departure plans, and when he leaves, Kerans and Bodkin discuss staying. That night, Kerans and Bodkin sink their testing station into the water and go to Beatrice's apartment. The next morning, Riggs arrives in the helicopter and tries to talk to them, but they don't listen. Riggs and the crew leave later that day, and Kerans realizes that he, Bodkin, and Beatrice will drift apart as their dreams consume their minds.
Six weeks later, Kerans wakes to see a man speeding around in a white hydroplane. Kerans gets in his catamaran and paddles closer. He climbs on top of a building and watches as three boats follow the hydroplane, along with several thousand alligators. Kerans tries to go back to his catamaran, but finds that the alligators destroyed it. He struggles on foot to Beatrice's apartment, where the two watch from her windows as Bodkin flags down the visitors. Kerans insists they have nothing to fear from these looters and goes to wave down the hydroplane.
Strangeman hosts Kerans, Bodkin, and Beatrice on his ship. He's perplexed that they want to stay in London and immerse themselves in their dreams. Kerans notices that Strangeman is albino, while his entire crew is black. Strangeman introduces them to the Admiral, his second-in-command, and offers to show them his treasure ship. The storerooms are filled with art and statuary. Kerans says that the treasures are like bones, and Strangeman rudely sends his guests away. Over the next two weeks, Kerans sees Strangeman often. Bodkin spends his time paddling the waterways looking for places he remembers from childhood, and Strangeman becomes convinced that he knows where there's hidden treasure. Strangeman hosts a diving party in the hopes of finding this treasure. He sends crewmembers down to the submerged planetarium, and then sends Kerans down. Kerans is entranced by the womb-like auditorium and the "stars" in the dome created by light shining through holes, but passes out when his air supply is cut off. He wakes on the deck, where Strangeman insists that Kerans tried to commit suicide.
A while later, Strangeman invites everyone to a party where there will be a surprise, and insists that it'll stop Kerans's "crazy time machine" (referring to the dreams). On the deck, Strangeman has a lavishly set table, in front of a Renaissance painting of Esther and King Xerxes. Kerans assumes that Strangeman intends for Beatrice to recognize herself in Esther. After dinner, Kerans asks about the surprise and Strangeman insists he's missing it. Kerans notices that the water level is going down: Strangeman has dammed the lagoon and is pumping the water out. Kerans and Beatrice are horrified, but Bodkin is entranced. When the water is gone, Strangeman's crew sets off looting and Kerans, Beatrice, and Bodkin walk the streets. They find the planetarium, which Kerans thinks looks like a sewer now that the water is gone. Kerans remains close to Strangeman for the next few days as he senses that Strangeman is becoming more dangerous. Bodkin tells Kerans to leave with Beatrice and soon disappears, but Kerans thinks he himself can't leave.
Strangeman's crew has little success finding treasures in London. One night, Strangeman tells Kerans that his crew thinks he' (Strangeman) is dead because he’s albino. Big Caesar sings for Kerans, but Strangeman interrupts him when he sees that Dr. Bodkin is trying to blow up the dam. Strangeman's crew chases after Bodkin, throws the bombs into the neighboring lagoon, and shoots Bodkin, killing him. When they return to Kerans and Beatrice, the crew seizes Kerans.
Strangeman's crew ties Kerans to a throne and tortures him for two nights. They leave him in the sun during the day and he barely survives. On the third night, they put the throne in a cart and wildly parade Kerans around the city. The cart rolls out of control and dumps Kerans facedown in the street. Sure that Kerans is dead, Strangeman and the crew leave. Kerans frees himself from the throne and manages to escape. Kerans hides in a building for a day before returning to the Ritz. The suite is destroyed, but Strangeman's men didn't find Kerans's gun in the safe. That night, Kerans sneaks onto Strangeman's ship and finds Beatrice in Strangeman's private chambers. Beatrice tries to make Kerans leave without her, but Big Caesar interrupts their fight. Kerans shoots him, and pulls Beatrice down the gangway and off the ship. They try to hide, but realize that Strangeman has them cornered. As Kerans is about to give himself up, Colonel Riggs and the army suddenly appear with machine guns.
Kerans speaks with Riggs the next day. Riggs insists that technically, Strangeman did nothing wrong and will likely be honored by the UN for draining the lagoon. When Kerans asks Riggs to re-flood the lagoon, Riggs acts as though Kerans is crazy and insists that all of them except for Strangeman and his crew are going to Camp Byrd tomorrow. The next day, Riggs and Strangeman make peace and Strangeman throws a party. Kerans attends but leaves early. When he sees that Riggs and Beatrice are leaving the party, Kerans plants bombs on one of the dams. Sergeant Macready sees Kerans do this and shoots Kerans in the leg. Kerans yells for Macready to get out of the way, but he dies in the explosion. The water rushes into the lagoon, sweeps over Strangeman, and upturns his boat. Beatrice runs to Kerans and tells him to leave. Riggs and Sergeant Daley chase Kerans, but Kerans escapes into the next lagoon on a raft. The helicopter searches for him the next day, but Kerans successfully hides. When it finally leaves, Kerans reaches an inland sea that will take him south.
Kerans travels south for several days as his gunshot wound gets worse and more infected. When he reaches the end of the sea, he tries to disassemble his raft and reassemble it, but cannot find more water to follow. He enters the jungle on foot and travels through the rain. Finally, he reaches a narrow valley with a rundown church in it. He discovers Lieutenant Hardman sitting at the altar, looking at the sun as it sets. Hardman is emaciated, blind, and doesn't recognize Kerans. Kerans cares for Hardman for three days and on the third morning finds that Hardman is gone. Kerans waits for several more days before moving on. He comes to another lagoon and stays there, in an apartment building, for a day. He thinks about his past and remembers Beatrice. Before he leaves, he scratches a note in the wall that he's okay. He knows nobody will read it. He heads south, and the narrator deems him a second Adam looking for forgotten paradises.
