1945: After serving as a combat nurse in France during the War, Claire Randall travels to the Scottish Highlands with her husband, Frank, so that they may become reacquainted after years apart. Their marriage feels the burden of unshared experiences, but though they may not be the same people they were when they married, they love each other and want to make it work.
While Frank busies himself with genealogical research, Claire pursues an interest in botany. One morning before dawn, Frank takes Claire with him to observe a ritual performed by a local group of druids at a circle of standing stones called Craigh na Dun. While looking around the circle afterwards, Claire spots a plant that interests her, but she and Frank make a hasty escape when one of the women returns to sit. Later that day, Claire decides to return to the circle alone to take a specimen of the plant. While there, a strange feeling overcomes her when she touches one of the stones, and she loses consciousness.
When she awakens, Claire discovers that the car is missing, and soon hears noises of what seem to be men engaged in battle. She runs through the woods until stumbling into a man that looks remarkably like Frank, but she realizes that the man's eyes are cold and unfeeling, nothing like her husband's. The man introduces himself as Jonathan Randall, Esquire, Captain of His Majesty's Eighth Dragoons – the name of an ancestor that Frank had been researching. Claire tries to run away, but the captain pursues her. Before he can do whatever harm he intended, another man knocks him out, and forcibly takes Claire with him.
The man takes her to a cottage, where many more men stand talking in a strange language, and one of them, Dougal MacKenzie, addresses her in English. He appears to be the leader, and spends little time interrogating her, but insists they must move soon and so must do something about Jamie before they go. The young man in question is injured, and just as a few men are about to force his dislocated shoulder back into place, Claire puts a stop to it at once and shows them how to properly mend the joint. As the party prepares to leave the cottage, Claire notices that she can't see the lights of Inverness, though Jamie insists they are looking straight at it, and it starts to sink in for Claire that she is no longer in the 20th century.
Their journey is delayed by another scuffle with the redcoats, and later by Jamie losing consciousness and falling off his horse, but eventually the group makes it to Castle Leoch, which looks quite different from the time Claire saw it 200 years in the future. She insists on bandaging Jamie's gunshot wound more properly, and when she sees the thick scars covering his back, he tells her about the first time he met Captain "Black Jack" Randall. Drawn close by this moment of intimacy, Claire backs off hastily, but from that point on feels friendly toward the lad.
Having been settled with a wash and clean clothes, Claire speaks with the Laird of the castle, Dougal's brother, Colum: a shrewd man who stands out because of a rare condition that Claire privately identifies as Toulouse-Lautrec syndrome. Though he demonstrates doubt about the strength of her story, he promises safe passage for her to Inverness in a few days' time. When Claire dines with the MacKenzies, she enjoys a little too much of Colum's strong wine, begins to lose the thread of her cover story while they subtly interrogate her, and commits a faux pas by assuming that Colum's son is Dougal's.
The next day, Claire visits Jamie at the stables, and over lunch he shares more about his checkered past. When she leaves, she discovers that Dougal's men have been keeping tabs on her, but when she confronts Dougal about it and reveals she intends to leave in four days' time, it seems like news to Dougal.
While collecting food for the kitchens, Claire is startled by Geillis Duncan, the wife of the procurator fiscal in the local village of Cranesmuir. Geillis confides that many people think she's a witch, but she demonstrates her knowledge of the local plants well enough. Later, Geillis accompanies Claire to the Hall, where tenants come to the Laird to settle disputes. In the matter of a girl's loose behavior, Jamie volunteers to take the girl's punishment. While treating the wounds on Jamie's face, Claire tells him she is leaving the following day.
While getting ready to leave with the tinker to travel to Inverness, Claire is detained by a summons from Colum to a dark, dank room, which Colum tells her is the surgery of the late Davie Beaton. Colum then informs Claire that she will not be allowed to leave, and she will stay on as physician for the castle.
As a guest-turned-prisoner, Claire contemplates what would happen if she told anyone the truth about how she came to be in the Highlands, and imagines that she would be deemed a witch or something similarly nefarious. Mrs. Fitz makes the suggestion that if Claire takes on the duties of a healer and does well, she will be in Colum's good graces, so Claire throws herself into her work, ever trailed by Dougal's spies. She learns of a boy that took ill and died, and asks why she was not summoned to help, but Mrs. Fitz explains that it was demons that killed the boy. Called to attend to Colum in his chambers, the laird asks Claire to massage his muscles to make movement easier for him, and she agrees.
Claire meets the young girl, Laoghaire, whose punishment Jamie took during Hall, during an evening's entertainment by the bard Gwyllyn. Even after Claire points out the girl to him, Jamie hardly notices Laoghaire, and insists on escorting Claire back to the surgery. There the two continue to feel a certain draw to one another.
When Claire learns from Geillis Duncan that Mrs. Fitz's nephew, Tammas Baxter, has taken ill, apparently the same way the other boy had, she takes it upon herself to examine the boy, but she is interrupted by the arrival of Father Bain, who intends to perform an exorcism. Later, while visiting Geillis in Cranesmuir, Claire witnesses a boy in the village square, awaiting punishment for an unknown crime. At Claire's urging, Geillis persuades her husband, the fiscal, to go easy on the boy, and he agrees – the boy will have an ear nailed to the pillory, rather than lose his hand for stealing. Horrified, Claire asks Jamie to help her free the boy without incurring the wrath of the surrounding mob, and together they create a diversion so that Jamie can remove the nail from the boy's ear.
Emboldened by their success, Claire asks Jamie to take her to the Black Kirk, where the alleged demons attacked Tammas and his friend. Claire discovers lily of the valley growing there, and suspects that the boys mistook the plant for wood garlic and ate it, not realizing it was poisonous. She returns to the Baxter cottage, where Father Bain tries to stop her from attending the boy, but Mrs. Fitz insists Claire be allowed to help. Claire administers a decoction of belladonna to counteract the poison, and Tammas recovers.
Later, Jamie tells Claire that Mrs. Fitz now calls her 'the miracle worker', and that now Colum would be loath to let Claire go any time soon. Dismayed, Claire fears she will never escape the castle, but her hope is renewed while enjoying another night of Gwyllyn's music. The bard sings the tale of a woman who traveled from a fairy hill to a distant land, but eventually returned to the life she left behind. Taking heart from the tale, Claire resolves to escape, or die trying.
Over the course of the next few days, preparations are underway for the coming Gathering, in which MacKenzie men travel to Castle Leoch with their families to pledge their loyalty to Colum. Intending to escape under cover of night while the men inside the castle drink and distract themselves with the goings-on of the celebration, Claire carefully plots her escape, stowing away food and provisions for her journey and throwing distractions at Rupert and Angus, her erstwhile compulsory escorts.
She dodges several obstacles (Mrs. Fitz, Laoghaire, and a drunken Dougal) but eventually makes her way to the stables, where she intends to steal a horse and flee the castle. There, her escape comes to a screeching halt when she trips over Jamie, who thinks Claire's plan was doomed to fail, considering the extra guards Colum had posted around the castle grounds. While he escorts Claire back to the castle, they are waylaid by a group of men, one of whom insists that Jamie take his turn to pledge the oath to Colum. After Jamie changes clothes and tells Claire his clan motto (Je suis prest– "I am ready"), Murtagh explains to Claire about clan tanistry, and the danger Jamie is in: if he pledges an oath to Colum, Jamie could position himself to succeed as Laird after Colum's death, which might give Dougal and his brother cause to kill Jamie to prevent that; if he doesn't, the MacKenzie clansmen would be outraged, probably enough to kill him.
Jamie finds a suitable middle ground at the oath-taking: while he cannot swear an oath to Colum, Jamie pledges his obedience to him as ally and kinsman, so long as he is on the lands of the Clan MacKenzie. Colum seems to accept this, and the clansmen do as well.
During the hunt the next day, a man is fatally wounded, and Claire speaks soothing words to him while Dougal holds the man until he dies. Later, Dougal inserts himself into a rough game of shinty with Jamie, Murtagh and Angus.
In her surgery, Claire goes about her work, her hopes of escape diminished until Dougal visits to inform her that she will accompany him and his men on the road while they travel through the MacKenzie lands to collect rents. It is on this journey that Claire meets an elderly lawyer named Ned Gowan, whose asthma she treats. Ned explains the process of collecting rent from the tenants, and that many of them pay in goods rather than money. While she appreciates Ned's companionship, Claire feels excluded when the men speak Gaelic so that she cannot understand them, but Jamie reassures her that the men don't hate her, they simply don't yet trust her.
In one small village, Claire joins a group of women waulking wool to pass the time. When Angus finds her enjoying a cool beverage inside a hut with the other women, he drags her back outside angrily. Claire retaliates in kind by taking back a milch goat that had been offered as rent payment, insisting to Dougal that one of the women has an infant and needs it more. Their argument draws attention but Dougal brushes it off, proclaiming that Claire is drunk. An Englishman approaches the scene and asks Claire if she is all right. After menacing threats from the Highlanders to mind his own business, Claire declines to ask for help and the man retreats to resume his redcoat uniform.
Later that night, Claire watches as Dougal conducts a second collection. She cannot understand his long speech in Gaelic, but is appalled when suddenly Dougal tears a huge rent in Jamie's shirt to reveal the scars on his back. After this display, the already impoverished villagers cough up more money for Dougal's purse. Claire voices her disapproval the next day to Ned, who listens good-naturedly but declines to elaborate on the matter further, letting her believe that her conclusion that Dougal is stealing from Colum is correct.
For weeks Dougal continues his routine, using Jamie's scars to garner sympathy, and money, from the MacKenzie tenants. On their travels they encounter a group of men burning a cottar's property and stealing from them, though none of the MacKenzie group intervenes. Murtagh and Ned explain to Claire that it's the Watch, who extort money in exchange for "protection" from the English, but in this case they are doling out justice to redcoat sympathizers.
At yet another village, Dougal shows uncharacteristic mercy to the tenants upon hearing that redcoats had looted the village just days earlier. Claire accuses him of going easy on the town just so that he can squeeze some money out of them later for his own purse, rather than the rents owed to Colum. Still, Ned lets Claire go on thinking she has everything figured out, and she steams in her indignation.
During that night's display, however, Claire recognizes the name "Stuart" in Dougal's speech, even though he's speaking Gaelic. She suddenly realizes the true intent behind Dougal's extra collecting: he's drumming up sympathy and raising money for the Stuarts, to support a Jacobite rebellion against the English. Claire is amazed that, so reluctant to give up the little they had earlier that day, the tenants now offer money for the Stuarts after Dougal's impassioned plea.
Claire's view of the Highlanders changes, seeing them now as rebels and patriots, rather than criminals, though ultimately she feels grief knowing the outcome of the coming rebellion, and the likely fates that await her companions in two years' time. On the road once again, the group encounters a pair of bodies, men crucified as traitors – undoubtedly the work of the English redcoats. They bury the men and continue on, stopping at an inn for the night. Trying to sleep, Claire hears a noise outside her room, and upon investigation she discovers Jamie outside her door. He explains that he wanted to be sure none of the drunken men from the taproom sought out Claire's bed that night.
The next morning, Claire reveals to Ned that she knows now that they're raising funds for the Stuart cause, and tells him they have no chance. They're interrupted by a brawl that breaks out among the MacKenzie group and other men, and Claire, while tending to the wounded afterwards, that they had fought in the name of her honor after the strangers had insulted her.
While the group packs up to move on with their journey, the mention of Culloden Moor recalls to Claire her harrowing visit to the field in the 20th century, with the knowledge that thousands of men, most of them Highlanders, were destined to die there. On another stop, while Claire washes at a stream, Dougal confronts her and demands again to know who she is, still convinced she is not just a lady from Oxfordshire. They are interrupted by the appearance of Lieutenant Jeremy Foster, the soldier who had asked Claire some days ago whether she required assistance. This time, he asks in the company of several other redcoated soldiers. Although Claire maintains that she is a guest of the clan MacKenzie, Foster insists she accompany him to speak to his commander. She consents, and Dougal goes with her.
At Brockton, Claire meets Brigadier General Sir Oliver Lord Thomas, commanding officer of the Northern British Army. Tension arises as the English officers at the table join Lord Thomas in openly mocking the Scottish people and Dougal himself to his face, but Claire chastises them and Dougal leaves to seek refreshment from the taproom downstairs. Over their meal, Claire explains her situation, and Lord Thomas seems sympathetic, even so far as to offer her an escort back to Inverness. Suddenly, Captain Jonathan Randall barges into the room; Lord Thomas objects to the amount of road dust on the man's uniform, and as Randall starts to leave, he catches sight of Claire and stares at her. They both claim no prior knowledge of each other, however, and Randall steps out into the hall to ostentatiously beat the dust out of his clothes.
After Lord Thomas conveys the gist of Claire's presence, he suggests that perhaps Randall could accompany her to Inverness. In the course of discussing the conflict between the English and the Scots, Claire slips up and ascribes ownership of the land to the Scottish people, and Lord Thomas corrects her, saying that it is the king's land. Though she backpedals to assure her loyalty to King George, Lord Thomas is clearly more suspicious of her. They are interrupted yet again, this time by word of a skirmish nearby that has left men severely wounded. Claire joins the surgeon to assist in an amputation.
When Claire returns to the room upstairs, she finds Randall alone, being shaved by a young corporal. Claire has a flashback to shaving Frank with the same razor, on one of their rare visits together during the war. Claire reasserts her desire to continue her journey to Inverness, though Randall demands, yet again, to know the truth of her identity and purpose in Scotland. She spins a tale about falling in love with and English officer and following him to the Highlands, only to discover the man was not in love with her, but lusted for her. She had just escaped the man when she encountered Randall in the woods. Randall counters that he will allow her to go to Inverness if she gives testimony against the MacKenzies, whom Randall knows to have been raising funds for the Jacobites. When Randall threatens to resort to less civilized methods of interrogation, Claire says she already knows of Randall's reputation in that regard, having heard of his laying a hundred lashes upon a hundred lashes on a "poor Highlander boy". Randall then proceeds to describe the circumstances she has referred to, in gruesome detail.
Though Claire is deeply disturbed and upset, she tells Randall there is hope for his soul if he chooses to be better, to choose right over wrong. Randall plants a seed of hope in her by suggesting he will let her be escorted to Inverness, but swiftly crushes it by punching her in the belly, knocking the wind out of her. When the young corporal from earlier comes upon them, Randall orders the young soldier to kick Claire repeatedly. Dougal interrupts and takes Claire away, though not before Randall declares that unless she is brought to Fort William the following day, the MacKenzies will be accused of harboring a fugitive, hunted and punished.
Dougal takes Claire to a spring to drink water, and again asks her for the truth about her identity. Claire maintains that she is just Claire Beauchamp, and finally Dougal says he believes her, now that she has drunk from St. Ninian's spring, a liar's spring. Dougal then explains that the only way to out of turning Claire over to the English is to change her from an English subject into a Scottish one, and to do that she must marry a Scot.
Later, Claire talks to Jamie about Dougal's idea to have the two of them wed, and Claire asks Jamie about his possible objections. He says that he isn't promised to anyone else, nor is he much of a prospect for a wife. In a last ditch effort, Claire asks if he might not object to the fact that she isn't a virgin, and Jamie replies that he isn't bothered by it, so long as she isn't bothered by the fact that he is a virgin. With that, Claire tacitly consents to marriage, and sets in to get as drunk as possible.
After the wedding, Claire and Jamie talk awkwardly with each other in the room designated for the consummation of their marriage. Through long hours of conversation, Jamie describes the preparations he undertook for their wedding – securing the offices of a priest, Ned's task of finding a wedding gown in a brothel, Murtagh finding a Fraser tartan for Jamie to wear, Rupert and Angus arranging for Claire's ring to be made from an old key – as well as stories about his family. Meanwhile, Claire reflects on her marriage to Frank before the war, and recalls that, after meeting Jamie for the wedding and learning his true name, she took off her gold wedding band and tucked it into her bodice. Claire and Jamie finally have sex for the first time, and Claire admits to Jamie, and herself, that she enjoyed it, and then feels guilty at the acknowledgement.
Claire makes the mistake of leaving the room to go down for food, and faces a room full of "witnesses" in the taproom below. Embarrassed, Claire retreats to the bedroom, and Jamie joins the men wearing only his shirt, to get food for himself and Claire. Dougal and the other Highlanders, much the worse for drink, offer advice to Jamie, who relays these later to Claire, and they share in the amusement. After discussing Jamie's day, and Claire admits she was quite drunk when the men roused her awake to get ready, Jamie asks if she remembers anything. She does, and together they recall saying their vows, Jamie outwardly calm and Claire terrified, followed by the blood vow in Gaelic.
They undress each other further, and have sex again. When Claire climaxes and cries out, Jamie apologizes, fearing he may have hurt her, but Claire explains that pain isn't necessarily a bad thing. She proceeds to perform fellatio on Jamie to illustrate what she means.
Later, Claire encounters Dougal in the now-deserted taproom, and he tells her that Randall has been informed of her change of legal status from English to Scottish. She is startled when Dougal begins to make advances on her, but she simply tells him, "I'm Jamie's wife," and leaves to return to the bedroom. There, Jamie gives Claire his mother's pearl necklace, and they make love once more.
The next morning, while shaking out her wedding dress, Claire's ring from Frank flies out onto the floor. She puts it back on, and looks down at her hands, her two wedding rings.
Back in the twentieth century, Frank returns to the police station in Inverness, having been instigating a search for Claire for the past six weeks. The officers there feel sorry for Frank, but insist that they have done all they can to find his wife, and the logical conclusion is that Claire left willingly.
In the eighteenth century, Jamie asks Claire if the feeling between them is usual for a relationship, and Claire admits that no, it is different from what she's experienced before. Suddenly an arrow flies through the air, and although they are wary at first, Jamie realizes that it is just his friend Hugh Munro, a licensed beggar. Hugh gives Claire a gift of a dragonfly trapped in amber, in honor of the couple's recent nuptials. Hugh also imparts some possibly vital information about a man who may have witnessed the murder for which Jamie was wrongly accused.