Richard Rahl, leader of the D'Haran Empire, has been captured by an Imperial Order commander, who lets him (under the guise of Ruben Rybnik) live if he will be the point man for the commander's Ja'La dh Jin team. During Richard's imprisonment, he is warned by a cloaked specter that he is now a player of the Boxes of Orden. Sister Ulicia is also visited by this figure, and is told that the time to open the Boxes has been reset to one year from the first day of winter-the day that Nicci set the Boxes into motion under Richard's name. The witch woman Six steals the third box of Orden from Nicci and Zedd. Zedd discovers that the Wizard's Keep is being affected by the contamination of the chimes, and places a spell to protect it from future damage.
Jagang's excavations in the Azrith Plains reveal catacombs under the People's Palace, which provide a secret entryway. Three Sisters of the Dark enter, killing Ann and capturing Nicci, while soldiers are sent into the catacombs to prepare an attack. The Sisters of the Dark discover what they believe to be the original Book of Counted Shadows. Taking the first sentence of the book literally, they give it to Kahlan, as verification of the book can only be guaranteed by a Confessor or a wizard, and KAhlan points out that the book is titled Book of Counted Shadow.
Upon a surprise visit from Jagang, who is sizing up the members of rival Ja'La teams, Richard disguises himself by covering the faces and bodies of his teammates and himself with intimidating symbols and parts of spell-forms. His team defeats Jagang's team in the tournament final, but Jagang, refusing to accept his team's loss, announces that the win is invalid after twice cheating in his teams favor. This decision causes a riot in the camp, during which Richard and Nicci escape and Kahlan is 'rescued' by Samuel. Richard and Nicci (helped by Adie) enter to the Palace through the catacombs, where Cara and Nathan help them wipe out the Order forces hiding there.
Rachel is lured into Tamarang by Violet, who has drawn a spell around her that sets 'ghostie gobblies' to destroy her. On her way, she is given a piece of chalk by Shota in disguise as Rachel's mother, and uses this to transfer the spell to Violet. Rachel then restores Richard's gift. She is again visited by the disguised Shota, who sends her to deliver a message with Gratch. Zedd is captured by Six, and discovers that the witch woman is in league with Jagang and has helped attack D'Haran forces in the Old World.
Richard is warned by Nicci that he must not reveal his love for Kahlan to her, lest Kahlan's lost memories alone fail to be restored, much like Richard, in the first book of the series, could not be told before finding the way to intimately love a Confessor while being untouched by her power. He then helps priestess Jillian give the Order's army terrible nightmares. Jagang is given particularly nasty dreams, mostly involving Nicci. Richard is taught many spells and spell-forms by Nicci, and then sends himself to the Underworld, using Denna as a spirit guide, and retrieves everyone's memories of Kahlan, but is attacked by the pursuing beast earlier sent against him, and attempts to escape by releasing Additive Magic into the Underworld, whence he is projected into a gathering of the Mud People. He is greeted by Rachel, who, with Gratch's help, had told the Mud People to hold a gathering to summon him. At the Palace, Nathan assumes Richard is dead and accepts Jagang's terms of surrender, which include surrendering Nicci to Jagang and giving the Order's magicians access to the Garden of Life in order to open the boxes.
Samuel attempts to rape Kahlan; during the struggle, she touches the Sword of Truth, which restores her memory of being a Confessor (though none of her other memories), and releases her power to take control of him. Samuel reveals he is an agent for Six, and that Richard and Kahlan were once married. He then dies when she refuses to forgive his attempt against her. Richard meets Kahlan on the way to Tamarang, but refuses to answer her questions about their marriage, for fear of contaminating the spell upon her. He gives her Spirit in compensation.
Six has imprisoned Zedd, Tom, and Rikka, and appears as Richard and Kahlan arrive in Tamarang to rescue them. Shota arrives, in disguise as Six's mother, as Six is about to recapture them. She kills Six and then Richard, Kahlan, and Zedd fly back to the People's Palace on the red dragon Six had enslaved; now revealed to be Scarlet's son Gregory, whom Richard saved as an egg.
At the Palace, Richard allows Jagang and his Sisters of the Dark to open the boxes of Orden. During the ritual, Jagang goes unguarded to Nicci, who locks a Rada'Han around his neck, rendering him powerless, and eventually kills him unceremoniously to prevent his martyrdom.
In the Garden of Life, the Sisters of the Dark discover the correct box and open it; however, they find a flaw in their success. Richard explains that all of the Books of Counted Shadows were false keys to the boxes; whereas if they had the true key, they would still fail by reason of malicious intent. Immediately, the Sisters are drawn into the Underworld.
Richard explains that the true key to the Magic of Orden is the Sword of Truth. Kahlan tells Richard she loves him, revealing that her emotions have contaminated her chances of regaining memory. Richard uses the Sword to reveal the correct box, which turns the blade white, and then splits it in half with the Sword to capture its magic. Now in command of life and death, he uses the magic to send the followers of the Order to a new world, devoid of magic; he then sends his half-sister Jennsen, her compatriots the Bandakar, and her suitor Tom after them, along with all who willing want to live in a world without magic. He also uses Orden to repair the damage caused by the chimes, and to send Chainfire to the new world he has created, ensuring the complete removal of magic from that world, and removing all its inhabitants' memories of their previous world. As Richard goes to close the opening between worlds, he fears Kahlan is lost to him; she, however, replies that she was protected from this loss because she had fallen in love with him on her own, much as he had with her from the beginning.
An epilogue shows Tom and Jennsen expecting a child, who will carry the Rahl name, and shows the emigrants gradually forgetting Richard and everything from their previous world. The book ends with the marriage of Cara and General Meiffert. It is revealed that the Sisters of the Light have moved into the Wizard's Keep, where along with Zedd, they can continue to teach young wizards. Chase (now a Warden of the Keep) and his family have also moved into the Keep, as have Adie and Friedrich, who are now a mated pair. Under Zedd's questions, Richard admits taking Panis Rahl's spell from red fruit, so that it is no longer poison, and to bringing back the Temple of the Winds to the world of the living, along with all sorts of other things. After Cara and Benjamin's wedding, the devotion bells begin to ring. Richard prevents the people from kneeling, arguing that they are no longer his subjects.
