Petaybee is a sentient planet that can control everything on its world and knows all the inhabitants who live on it. When the Company Corps soldiers arrive in what is supposed to be a sneak attack, they find the village of Kilcoolie empty, the inhabitants in the communal caves where the people speak directly to Petaybee. When the soldiers try to spread out to look for them, the planet sends a storm that keeps them confined to the ship and the longhouse.

In the cave, Yanaba notices her two children, Ronan and Muriel, are gone. They are in the city-ship that belongs to a race of non-human shapeshifters that was on the planet before the humans arrived. They are taking them to Versailles Station, which is owned by Marmie, Petaybee's influential friend. She was falsely arrested and sent to the prison planet Gwinnet, and the Petaybeans can't contact her influential friends because of atmospheric conditions. When they reach the station, they have only minutes to send out a message because the Corps has arrived, arresting everyone and sending them to Gwinnet. Ronan and Muriel are taken there and are separated from the adults, who go to the hardcore prison where Marmie is while their children go to a prison youth camp.

On Petaybee, Yanaba has a plan to hijack the spaceship to get help and then locate the children and Marmie. They are successful and the ship lifts off to go to the authorities to report the crimes against Marmie and Petaybee.

On Gwinnet, the Selkie children are able to escape with the help of the other children. After almost being eaten by a giant squid they are let go after being caught in a fisherman's net. Ronan is caught by their old enemy Professor Mabo who knows he is a Selkie. She plans to perform torturous experiments on him and she puts a pain collar on his neck to control him. Muriel is frantic to find her brother and rescue him and she has the sympathy and help of the people and the alien lifeforms.

What began in Changelings and continued in Maelstrom comes to a glorious conclusion in Deluge. Although this can be read as a stand-alone novel, readers who want more background information would be better off reading the first two books in the series, which describe the alien lifeforms in the city-ship in great detail.

Anne McCaffrey and Elizabeth Ann Scarborough are known for creating believable sentient alien lifeforms, especially the legendary Ms. McCaffrey with her Pern series. The aliens in the city-ship play a very important role in the novel because they help their good friends Ronan and Muriel. Although Ronan and Muriel are twins, they have distinctive and different personalities. He is impulsive and she is the careful one who thinks before she acts. They communicate with each other and the aliens telepathically, which is a great plot device because it hides their true intentions from their enemies.

The novel spotlights three unique groups: Marmie and her people from the station; the inhabitants of Petaybee; and the twins and their allies, including a very special cat and a shape-shifting sea otter. The action shifts from one group to another so seamlessly that the audience doesn't even notice. The villains of Deluge, from the corrupt prison officials to the crooked Corps, are also three-dimensional characters, as readers know what motivates them (greed and power), and though readers want them defeated, they want the punishment to fit the crime as some are more guilty than others. Although the tale targets teens, adults also will thoroughly enjoy this magnificent spacefaring novel that warns people to stay alert over the actions of the powers that be.