Ralph returns to Petranilla, curious but still uncertain about her story. She confirms it once more, claiming he has the blood of a warrior, born to greatness. He laughs bitterly and tells her about the peasant rising in Wigleigh. Petranilla is unconcerned, because such events can be put to good use.
Caris confides to Merthin that when she finds a successor she'll give up the priory and go away with him, but he isn't sure. She's changed her mind before.
When Ralph informs Isabella about the rebellion, he points out that only the Earl of Shiring has authority to deal with the matter, and slyly points out that Roland died of plague. Petranilla steps in with another proposal. The female Prior at Kingsbridge clearly has illegal ideas - giving land to peasants and luring them from their rightful masters is a dangerous practice. Perhaps a new bishop could strip her of authority, and Petranilla knows just the man: Godwyn, naturally.
When Ralph enters Shiring Castle, it's as if he owns the place, and to Philippa's horror he does. He's also authorized to take a wife, and that can be either her - or ten-year-old Odila. The choice rests with Philippa. She gives in.
Caris shows Merthin her completed book, more comprehensive than he dreamed possible. Their joint delight leads to lovemaking, despite being in the Priory building, followed by sleeping together behind the locked door of her office.
In his new bishop's robes, Godwyn conducts the marriage service between Ralph and Philippa, but it's destined never to be consummated. As she lies in a steaming bath on their wedding night, Philippa tells Ralph how she's sent Odila out of his reach, then shows how she slit her own wrists. Soon she is out of reach as well.
Godwyn has his men burst open Caris's door. He intends only to have her removed from office, but gains a bonus when he finds her sleeping naked in Merthin's arms. She's very clearly broken her vows, and Godwyn takes sadistic pleasure in branding them both: "F" for fornicator and "W" for whore.
Thomas arrives to find the wounded couple packing, determined to leave Kingsbridge once and for all. He wants them to stay and stand up to Godwyn, but Merthin wants to know why Thomas never does that for himself. The accusation is like another brand, stinging him to action first by writing a formal document, then recovering the object he buried so many years ago. The document is that long-sought borough charter for Kingsbridge, and the object is a velvet purse containing the Royal Seal of King Edward II. Merthin and Caris finally realize who Thomas really is. A flashback reveals what he partly described: surrender and imprisonment, attempted murder and disguised escape to the town of Kingsbridge. The charter is an overdue reward for loyalty.
Godwyn claims to know how such an old document looks so fresh and promptly arrests Caris on the old witchcraft charge. No longer a nun, she has no protection against what he plans for her. Meanwhile Ralph and Petranilla show the seal to Isabella, alarming her with confirmation that the husband she tried to murder is very much alive. She uses this evidence and the Wigleigh rising to force Edward III into action against an apparent hotbed of rebels before it flares into another civil war. He musters troops to destroy Wigleigh and Kingsbridge, while Isabella and Ralph come with him to ensure it's done thoroughly.
In Kingsbridge Godwyn has condemned Caris to be burned as a witch. She appeals to Petranilla to intercede, only to learn that mother and son are united in their hatred of her. But Thomas confronts Godwyn, describing and defying his corrupt authority. The crowd of Kingsbridge and Wigleigh citizens is fully behind him, overwhelming the soldiers, and though Godwyn tries to light the pyre as he flees, Merthin is released from the stocks in time to rescue Caris. But then Sam comes running with a warning: the King's army has attacked Wigleigh, and they're surrounding Kingsbridge right now.
Ralph rides onto the bridge and pronounces a General Arrest; everyone in the town is guilty of revolt and sentenced to death. There will be no mercy, and when the archers start to shoot they show none. Thomas urges the citizens to fight rather than be slaughtered, and with no other choice they arm and prepare to go down fighting. Petranilla tells Godwyn about his illegitimate brother Ralph, but doesn't get the response she expects; after the battle he promises to hang her as a whore.
The battle begins, and the King's army sets about breaking through the town gate and scaling the walls. Despite valiant resistance they succeed, pouring into Kingsbridge, killing as the go. Holger, Sam, Gwenda, Wulfric, Merthin and the rest fight furiously, while Caris runs to the Priory to rescue her book. There she finds Petranilla, dying from the poison she took to escape whatever lunacy Godwyn has in mind. Caris tries to help until Petranilla, hate-filled to the last, admits how she murdered Caris's parents. But instead of cursing or weeping, Caris simply begins to pray for Petranilla's soul. It is kindly meant - and yet it is a perfect revenge.
Ralph cuts Holger down, then goes for Merthin and the two fight savagely. Sister Mair falls to an arrow, and finally Edward III meets up with Thomas and they go at it sword to sword.
Godwyn finds Caris with his mother, and attacks her as if nothing else is happening outside. Caris frantically fights him off with bottles, furniture and finally with a metal crucifix, smashing his skull with the symbol whose authority he has abused for so long.
Merthin gets Ralph on the ground, but is too decent to kill a helpless man, unaware of his hidden dagger. Sam has no such qualms and puts an arrow through Ralph's throat.
Thomas tells his son that he is willing to die if Kingsbridge is spared. Edward III gives his word, and Thomas lets himself be killed. Immediately Edward gives the order to withdraw, and the army rides away with the King at its head and Isabella trailing behind. The people of Kingsbridge - Wulfric, Gwenda and Sam among them - watch, realizing they have survived while Caris and Merthin embrace, able to pick up the threads of their lives again.
And within a generation, the stand taken at Kingsbridge will be echoed in the great Peasant's Revolt that changes England forever.