Richard Rahl is the ruler of the D'Haran Empire, a collection of nations previously made up of D'Hara, the Midlands and Westland. Richard Rahl and the D'Haran Empire are currently locked in an epic struggle with the Imperial Order, an Empire from the Old World, led by Emperor Jagang.
Chainfire continues the story of Richard in his attempt to teach the people that their lives are theirs alone, and that they can be free of the Imperial Order. Richard is gravely injured from an enemy's arrow. He is brought to Nicci, a sorceress and former Sister of the Dark, who heals him using subtractive magic; this causes unforeseen events to spiral out of control. When Richard awakens, he discovers that his wife, Kahlan Amnell, the Mother Confessor, is missing. More than that, however, no one around him seems to remember her. Nicci and Cara both attribute Richard's memory of Kahlan to dreams and delusions brought on by his injury and quite possibly an unintended effect of the subtractive magic used in healing Richard. Despite Richards attempts to explain the events of the last several years could not have happened without Kahlan, the paradoxes are explaiend away as Richard remembering things wrong.
Fearing for Kahlan's life, Richard desperately tries to find some trace of her and at the same time convince the others that she exists. His search leads him to the witch woman, Shota, who reveals "that which you seek is long buried with the bones". In return for more information, Shota demands the Sword of Truth, which Richard relinquishes to her pet, Samuel, the previous bearer of the sword. Shota then utters the words "Chainfire" and "The Deep Nothing" and tells Richard to "beware the four-headed viper". She also warns Richard of a "blood beast" conjured by several wizards and Sisters of the Dark, under the orders of Jagang. The beast is meant to kill Richard and is as unstoppable as it is unpredictable. Further, the beast is able to track Richard when he uses his gift because of the way Nicci healed his arrow wound.
In the meantime, Ann and Nathan together have discovered many blank pages in books of ancient prophecy. They seem to remember that the pages should not be blank but cannot remember what was originally written there. Zedd makes the same discovery independently.
Concerned, but still determined to find his wife, Richard makes his way to the Wizard's Keep to find Zedd, who has no memory of Kahlan either. To try to prove her existence, Richard exhumes her grave and is shocked to find a corpse in the buried casket with a nametag attached to her dress. He is destroyed and debates killing himself, and Zedd, Nathan, Nicci, and Ann consider using Nicci's subtractive magic to delete Ricahrds "delusions", but Nicci convinces him to persevere. Ann, Nathan, and Nicci make their way to the Keep as well and are reunited with Richard, Zedd, and Cara.
As Richard continues to attempt to prove the existence of the woman he loves, the others become convinced that he is mentally ill and plot to "heal" him, so that he will 'fulfill prophecy' and lead the D'Haran army against the forces of Emperor Jagang. At the same time, the reader learns that Kahlan has been kidnapped by the four remaining Sisters of the Dark who escaped the Dream Walker in Blood of the Fold. The Sisters have cast a spell using subtractive magic to erase people's memories of Kahlan and Kahlan's memories of herself. The Sisters then use Kahlan to steal the boxes of Orden from the Garden of Life in the People's Palace.
Richard, Nicci and Cara, make their way to the Sliph in order to escape the Keep and what their enemies will do. Richard learns that the Sliph knows of a place called the Deep Nothing. The Sliph takes them to some ruins called "Caska" in the Deep Nothing. Upon arriving, they find themselves in the midst of a group of Imperial Order advanced scouts that have captured some of the people there. The reader is introduced to a girl named Jillian and a people called the "Dream Casters". While Nicci eliminates the Imperial Troops, Richard and Jillian look for answers in the catacombs. Together, they find a hidden passage that leads to a protected library. In the library, Jillian discovers a book titled Chainfire.
They travel to the People's Palace and learn that the boxes are missing and that they have been put into play. Richard figures out that the Sisters have stolen his wife and the boxes. While there, he learns that an older woman has been captured and that there is something uniquely odd about her. As Nicci investigates, she discovers that it is Sister Tovi, one of the Sisters of the Dark who gave an oath to Richard in order to be free of Jagang, the Dream Walker. Nicci uses deception to learn everything she can from Tovi, discovering that it was Samuel who stabbed Tovi and took the Box of Orden she was carrying. She also learns about the Chainfire spell, about how it was used to obliterate everyone's memory about Kahlan, and that the Boxes of Orden were created in opposition to it. Later, Richard realizes that the Sword of Truth protected him from the Chainfire spell, which is why he was still able to remember Kahlan.
Richard, Nicci and Cara return to the Wizard's Keep and, with the information gathered from Tovi and the book "Chainfire", they finally manage to convince Zedd, Nathan, and Ann of the truth. While no one but Richard remembers Kahlan, at least they now believe that she exists.
