Finn is a prisoner in Incarceron with his oathbrother Keiro. While stealing from some other residents of the prison, the Maestra comments that she once saw the birthmark on Finn's arm upon a crystal they recently discovered. Finn, who has no memory since waking up at the age of 15 in a cell in Incarceron, keeps her alive to learn more about this crystal.

Finn frequently suffers from seizures and fits during which he sees visions of the Outside, which make him believe he is from the Outside. Gildas, the old Sapienti who is a part of the same crew as Finn, calls him Starseer, and believes he will lead them out of the Incarceron. Keiro, Finn, and Gildas all combine to convince the leader of the group to ransom the Maestra for her weight in treasure, including the key. They do so, but at the end they are betrayed, and the Maestra is killed, but Finn gets the key. He is wracked with guilt due to his promise to keep the woman alive.

Finn, Gildas, and Keiro decide to leave with the crystal, which Finn recognizes as a Key, but when their plot is discovered, they must fight their way out. Keiro is about to be killed by the bandit leader when his dog slave who tests the food to ensure it isn't poisonous, distracts him long enough to give Keiro the upper hand. Attia, the slaves name, joins the three as they began their journey to escape the prison.

Outside the prison Claudia prepares for her impending marriage to the prince, while planning a way to avoid it with her close friend, tutor, and Sapienti named Jared. Together they are able to break into her father's (the Warden of Incarceron) study where she steals a key that is the same as Finn's. Using it, she begins to be able to communicate with Finn and they work towards helping him escape.

Through their conversations, and some outside investigation, Claudia begins to think that Finn is Giles, Prince Caspar's brother, and the man she was originally betrothed to before his mysterious death.

Finn and the others continue their attempts to escape, and they meet with a Sapienti who rescues them from a giant snake incarnation of the prison. In the mysterious Sapienti's flying castle they discover books that appear to show the lives of ever prisoner who has ever been in Incarceron, through a series of pictures taken by the prison. Finn finds his life starts only a few years ago. Attia discovers that Claudia was once a prisoner, but was removed at birth. She tells no one of this.

Claudia's wedding to Prince Caspar is moved forward, and out of desperation, she enters Incarceron from her father's study to try and rescue Finn and set him up as the true heir to the throne. Incarceron, it turns out, was built using advanced shrinking technology and is actually upon a bracelet the Warden wears. Claudia finds Finn and the others, but the Warden (the mysterious Sapient in the flying castle) and the prison fight to stop them from escaping. Only Finn and Claudia make it out, leaving Attia and Keiro trapped inside Incarceron. Finn has promised to return for them.