Jamie, injured, is in company with Dougal and his men when Murtagh brings an Englishwoman back to the cottage where they are hiding from the redcoats. Claire Beauchamp seems strange, even for a sassenach, but knows enough about healing to mend his dislocated shoulder and bandage his gunshot wound. The men leave the cottage, taking Mistress Beauchamp along with them to share Jamie's horse. They're halted once more by another encounter with the redcoats, and in the course of the fight Jamie is injured again. He doesn't let on to Claire how bad it is until he falls off his horse, wearied by blood loss and fatigue. She mends his new bayonet wound before the band sets off again, riding through the night before they reach Castle Leoch after dawn.
While Claire tends to Jamie's shoulder with a clean dressing and bandage, he tells her the story of how he knows Captain Randall, and the two share a moment of intimacy. Jamie promises that she need not be scared as long as he's with her.
Jamie spends the coming weeks away from the castle, choosing to sleep in the stables at night and break horses by day. He does attend Hall, however, and volunteers to take a young girl's punishment. He chooses fists against Angus Mhor, dealer of justice at Hall, and Claire and Mrs. Fitz tend to his bruised face with leeches. Over the following weeks, Claire takes to visiting Jamie at the stables, and he shares bits of his past with her.
With preparations and celebrations underway for the Gathering, Jamie tries to stay scarce even more than before, in an attempt to avoid making any kind of declaration of loyalty to the MacKenzies. Fate intervenes, however, and Claire stumbles over Jamie in her own escape attempt. He escorts her back to the castle, and in the process several MacKenzie clansmen make sure Jamie gets ready for the oath-taking. Despite the delicate situation, Jamie navigates it ably, pledging his obedience to Colum so long as he's on MacKenzie lands, but admitting that his clan loyalty lies elsewhere.
After the Gathering, Jamie joins the MacKenzies, as well as Claire Beauchamp, on the road to collect rents from the tenants that couldn't make it to the Gathering. In the course of their travels, Dougal uses Jamie's back scars to make an example of him while drumming up support for the Jacobite cause. Claire offers Jamie advice on finding an outlet for rage by hitting something. Later, during a night at an inn, Jamie sleeps outside the door of the room Claire is staying in to guard against drunken English soldiers.
After Dougal has taken Claire to meet with Captain Randall at Fort William, he determines that the only way to protect Claire from the Captain's ill intentions is to marry her to a Scot, and that Jamie is the best man for the job. Claire protests the plan, but relents, lacking any better ideas.
Jame reveals to her his full name just before the wedding ceremony, which takes place in the same small church where she and Frank were married almost two hundred years in the future. Claire, stunned by the quick turn of events, finds solace in married intimacy with Jamie, who reveals that he has been in love with her for some time, and was more than happy to marry her.
Jamie reveals much more of his past, including his childhood in Lallybroch and the years before he was sent to France to join the army. He tells Claire the events of his life which involved Jack Randall, including arrest, the rape of his sister, floggings, and homosexual advances. Jamie and Claire grow closer and closer as the group travels around the countryside, and by the time they reach the location where modern-day Inverness would be located, Claire is very much in love with Jamie. Regretting that she will break his heart by running away, she tries to reach Craigh na Dun on her own and return to Frank. She is caught, however, by one of Jonathan Randall's staff, and is brought to the English fort he commands.
Jamie and the other men rescue Claire from the English, committing arson, murder, and assault in the process, and flee back towards Castle Leoch. Claire doesn't at first realize what serious danger she caused, and is furious when Jamie calmly announces he must beat her for disobedience. Afterwards, however, the other men treat her more kindly than before, and she and Jamie make up when he tells her stories of being whipped for disobedience as a boy, although she threatens to disembowel him if he does it again.
The group returns to the seat of Clan MacKenzie, where Claire encounters the now-jealous Laoghaire. Jamie finally buys Claire a wedding ring, a woven silver band engraved with thistles; she wears it on her right hand, opposite Frank's gold wedding ring. Claire becomes friends once again with Geillis Duncan. One day, they encounter a child abandoned on a hillside. Claire's natural compassion moves her to try to save the child, but Geilie stops her, saying the parents consider it a changeling. She is seen with Geillis and Jamie on the hillside; the child later dies. Geilie's husband mysteriously dies a few days later, and before Jamie leaves on a stag hunt, he warns Claire to stay away from the widow, since she is now rumored to be a witch.
When the trial begins, Ned Gowan arrives to defend Claire; his efforts lead the judges to have the women thrown in the lake (to see if they float) rather than burning them outright, but Claire's sharp objections cause them to have her flogged. As she is being whipped, Jamie arrives and dramatically throws a set of jet rosary beads onto her neck, proving that she could not be a witch. Geillis helps to distract the crowd by proclaiming that she, but not Claire, is a witch: as Geilie strips off her gown to reveal her secret pregnancy (saving her from being executed), Claire sees a vaccination scar on the other woman's arm, proving that she, too, is a time-traveller from the twentieth century.
Claire confesses everything to Jamie after they flee Cranesmuir, telling him about her time-travel and why she is not technically a witch. Jamie accepts everything, and takes Claire to Craigh na Dun, urging her to return to the twentieth century. She is torn between going back to Frank, from whom she has been missing for almost six months, and staying with Jamie, whom she has come to passionately love. With a great deal of torment, she eventually chooses to stay with Jamie, and he takes her to Lallybroch.
Upon reaching Lallybroch, Claire meets Jamie's sister, Jenny, who is enormously pregnant and has a small child named Young Jamie, after his uncle. Jamie, thinking that Jenny was raped by Jack Randall several years before, accuses her of standing as the Captain's "doxy," and a terrible fight ensues. Claire escapes from the room and meets Jenny's husband, Jamie's best friend, Ian Murray: the two immediately like one another, and manage to settle their respective spouses down.
Claire becomes fast friends with Jenny, and happily settles into Lallybroch. Settling into life at Lallybroch also meant for Jamie taking over being the laird. As this went to his head he accosted a tenant, Ronald MacNab, resulting in his son Rabbie being taken in as a stable boy. As retribution, Ronald turned Jamie over to the Black Watch - who take Jamie while he is out with Ian. As Claire and Murtagh search for him Jamie awaits his hanging at Wentworth Prison. A death which he would have taken over Jack Randall 'rescuing' him from the noose and torturing him instead. After Dougal is able to find and tell Claire where he is, she along with Rupert and Murtagh concocts a plan to rescue him from the prison.
Claire sneaks into the prison and finds Jamie in a small room, already suffering from torture by Jack Randall. She has almost freed Jamie from the room when Randall himself enters with a servant, and holds Claire at knife point; Jamie promises to resist neither Randall's sexual advances nor his torture, in exchange for Claire's freedom. Jamie suffers greatly physically, emotionally, mentally, and spiritually at the hands of Jack Randall.
With the aid of Marcus MacRannoch, an erstwhile suitor of Jamie's mother Ellen MacKenzie, and upon Murtagh's and Rupert's arrival, agrees to help rescue Jamie. The Scots release a large herd of cows into the same door through which Claire exited, and in the ensuing stampede Jamie is found and brought unconscious to MacRannoch's house, having been further raped and tortured by Randall.
Claire manages to doctor Jamie's injuries, the worst of which his badly broken hand. They depart for France; between his injuries, being waylaid on the road, suffering through terrible seasickness on the Channel, Jamie is seriously ill by the time they reach the Abbey of Ste. Anne de Beaupré, where his Fraser uncle, Alexander, grants them sanctuary. During Jamie's illness, Claire befriends the Benedictine monk Father Anselm, who counsels her in the religious aspects of marriage: she also confesses her true past to him.
Jamie suffers terribly from the memories of being raped by Jack Randall; he asks Claire to leave him and return to Scotland, since he can't think of her without remembering Randall. But before he can force her to go, Jamie's hand becomes infected. In the subsequent delirium of fever he asks Claire to let him die, which he later admits was because he thought she would amputate the hand. "Damned if I will," Claire says; using opium and the memories of Jack Randall as shock treatment, she brings him through the fever and into convalescence. The novel ends with Jamie recovering from his illness and planning to take Claire to Paris, and her confession that she is pregnant.