Book 2 of the Atherton series.
In this book, the three children; Edgar, Samuel, and Isabel part ways as the highlands continue to sink into the center of Atherton and the cleaners invade. The story continues to take place on Atherton, although the central levels are sinking and new underground areas are discovered. This is also the first book in the series where characters die.
Plot Spoilers!/summary
As the levels of Atherton continue sinking into each other, Samuel and Isabel are captured by Lord Phineus and Sir Emerik. This whole time, Lord Phineus has become more agitated and unstable. Edgar, Vincent, and Dr, Kincaid travel throughout tabletop, and warn of the coming army of cleaners. Eventually, they reach the highlands and are captured, and forced to journey with Lord Phineus, Sir Emerik, Samuel and Isabel to the source of all water on Atherton, through a secret passage. Inside, they are warned to keep to the yellow line, to avoid being lost. As they go on, the group is attacked by a group of beasts known as Krats, which have poisonous bites that cause madness. Emerik is bitten in the struggle, but goes on. Finally, the group reach the source of water, where they find Samuel's father, who is still alive.
On the surface, the villages discuss the attacks by the Cleaners, and begin making plans to evacuate to the flatlands to escape the sinking centers of Atherton.
They proceed to go into a strange labratory, where numbers are written everywhere including the ceiling. Lord Phineus has become more mild mannered, and gazes around with curiosity. Dr. Kincaid tells him to wake up, and when Lord Phineus denies it, Dr. Kincaid begins yelling out random numbers from on the ceiling. This causes Lord Phinius to break down. Dr. Kincaid reveals that Lord Phineus is in fact Dr. Harding, the creator of Atherton and Edgar's "Father". The numbers on the ceiling in fact represent different ideas and creations, locked in Dr. Harding's head. As the water continues rising, Edgar is kidnapped by Erik back to the surface, and Dr. Harding goes after him, while the rest of the group descends deeper into Atherton to escape the flood.
On the surface, Sir Emerik begins displaying the symptoms of madness caused by the Krat bite, and dies. The rest of Highlands having already evacuated, Edgar and Dr. Harding rest. Dr. Harding tells his story and brings out an emergency boat he had once made. Putting Edgar in the boat, Dr. Harding pushes Edgar out onto the ocean, and peacefully accepts his fate and death, dreaming of a boat on calm waters.
As the people of the surface battle the cleaners, the humans push towards the flatlands. Almost everyone makes it, and as they look back at the army of cleaners, the levels of Atherton continue sinking, trapping the cleaners. When the water hits the cleaners, their legs and teeth begin to dissolve, turning them into non aggressive, aquatic scavengers.
Underground, the group finds themselves in the Inferno, the fiery center of Atherton, filled with some of Dr. Harding's other creations, which he could not bear to destroy.Notable examples include the Lava eels, the Nubian, and the Fire bugs. As most of these are dangerous, the travelers must defend themselves, and barely have any time to rest.
Eventually, Dr Kincaid, Vincent, Isabelle and Samuel manage to make their way back up to the flatlands, where the remains of Atherton's civilization start anew with the remains of their village and flocks, and the cleaners swim peacefully in the dark central lake.