The novel takes place in a post-global warming future in which the Earth has flooded and the surviving population is controlled by a small group of people, "The Chosen," from a place simply known as "The Island." The story follows the main protagonist, 12-year-old Spider, who lives with his family on a houseboat. One day, after Spider comes home from yet another unsuccessful day of fishing, he learns that his twin brother Luke has been arrested for trying to start an uprising against The Chosen with the neighboring HouseBoaters.
While out fishing the next day, Spider discovers a mysterious pipe that he swims down, which leads to an underwater greenhouse. There he befriends a girl named Ruby and realizes that the world is much larger than he had previously known: a whole community lives deep down in the ocean, and these people (known as AquaGrowers) are also controlled by The Chosen.
With the help of Ruby's grandfather, Spider and Ruby leave the underwater greenhouse and set sail for The Island to find and free Luke. Along the way, they get held hostage by a band of marauders, manage to escape at the last moment, and eventually make it onto The Island where they hide in the back of a truck that takes them further inland. They end up in a giant kitchen where they befriend a cleaning woman named Josephine who smuggles them back to her modest shack in her cleaning cart. They witness first-hand and Josephine tells them about all the injustice on The Island. Just like AquaGrowers and HouseBoaters, The Chosen control two groups of people on the island: Preparers and Servants.
Spider and Ruby join Josephine's children in school the next day, but soon are arrested and thrown in prison. There they finally find Luke, and the three escape by scaling the prison wall. They make their way back to Josephine's shack and are betrayed by one of her neighbors, but they manage to steal a prison van and take off to the remote part of the island where an old friend of Ruby's grandfather, The Engineer, lives. They need The Engineer's help if Luke is to continue his efforts to organize the AquaGrowers and HouseBoaters in a revolt against The Chosen.
Spider, Ruby, and Luke arrive at The Engineer's house and smuggle her out disguised as ambulance drivers who have come to take her to the hospital because she has fallen ill. They eventually make it to a rigged annual competition where it is "decided" who will be Chosen, Servants, and Preparers for the coming year. Spider and Ruby join the competition as contestants and, after many trials and tribulations, manage to win it. However, they get disqualified and decide to expose all the injustice that they have witnesses on The Island. They do so via a microphone booth on the highest tower on the island.
Meanwhile, Luke triumphantly returns to The Island with hundreds of AquaGrowers, HouseBoaters, and even a few marauder boats in tow. The Chosen relinquish their power without a fight and a new and better future for all the people off and on The Island is on the horizon. The main characters in the novel gather in Josephine's modest shack and celebrate their newfound peace and freedom.
At the very end of the story, Spider steps outside to stretch his legs and notices that it is steadily getting warmer, just like it did all those years ago when the planet first started to flood. He wonders how long they can manage to survive, no matter how well everyone gets along. This creates the opening for a sequel where Spider and Ruby go on a quest to find a solution to global warming before it's too late.