It has been a week since Trenton and Kallista left their mountain city of Cove--now renamed "Discovery"--aboard their homemade mechanical dragon to search for Kallista's father, Leo Babbage. They find a compass and clues that point them towards a second underground city. Hoping to find Kallista's father there-and perhaps more information about the living dragons that ravaged the world-they head west, thinking they will find a thriving city like Discovery. Instead, they find only large swaths of blackened forest and the ruins of destroyed buildings, and a small civilization.
Trenton and Kallista are quickly captured. They find themselves embroiled in a civil war between a clan of scavengers and hunters called Whipjacks, and the Order of the Beast, people who believe that dragons are divine and were sent to cleanse the world of evil.
Trenton and Kallista learn that Leo is also being kept prisoner and that he is being forced to make weapons for the civil war. They try to free him but fail and are recaptured. Before they can be sacrificed by the Order of the Beast to the red dragon, they escape and travel back to Cove to warn them of an impending attack by both the Whipjacks and the Order of the Beast.
The people of Discovery fight back, but they are outmatched. Trenton and Kallista manage to power up a laser beam that allows them to prevail, and the Whipjacks and members of the Order of the Beast are imprisoned.
The citizens of Discovery have built two more mechanical dragons based on Leo's original blueprints, but they have been modified and are now armed with gunpowder weapons. However, more live dragons are showing up every day, so the people of Discovery decide to blast the mountain entrance closed for safety. But it is only a temporary measure, and Kallista, Trenton, Leo, and a few others must go in search of the source of the dragons to put an end to the threat once and for all.