Roger is in the middle of sorting through his recently deceased adoptive father's estate, when Dr. Claire Randall and her daughter, Brianna, arrive at his door in Inverness in 1968. While ostensibly in Scotland to do sightseeing, Claire asks Roger about a list of men who fought at the Battle of Culloden in 1746, and wants to know if any of them survived.
Glad to have a distraction from sorting through all the late Reverend's books, papers, and other belongings – and rather taken with Brianna Randall – Roger agrees to look into Claire's query. Still, he can't shake the impression that Claire Randall is holding back more than she is letting on about her research request. Claire also tells Roger and Brianna about the time 20-odd years before that she and Frank watched a local group of self-styled druids dance on the fairy hill of Craigh na Dun, and asks Roger if the late Mrs. Graham has any family who might be available for Claire to talk to. Roger says there's a granddaughter, Fiona Graham, who took over at the manse after her grandmother passed.
When Roger mentions possibly stopping by the stone circle on a trip to Broch Tuarach, Claire knocks over a glass of whisky, spilling it on Roger's trousers. After a tense moment of allowing Brianna to pat him down with napkins, Roger has the strange notion that Claire might have knocked the glass over on purpose.
Roger continues to be distracted from cleaning up the manse, wishing to dig into Claire's research project, though not so much for the project itself, than that he might use it as an excuse to see Brianna Randall again. He decides to visit Culloden House the next day.
The question of Claire's list of men at Culloden grows ever more curious after Roger finds puzzling inconsistencies regarding the men of Broch Tuarach, as well as the usual difficulties of finding a specific person in the historical record among countless others with the same name. Certain that Claire had deliberately prevented him from inviting Brianna to join him on his trip to Broch Tuarach, Roger has a historian's urge to find out what exactly is going on with Dr. Randall and this project, as well as a keen personal interest in seeing Brianna again.
In pursuit of more leads, Roger travels to Edinburgh with just one clue: the name Captain James Fraser, which had not appeared on Claire's list but had linked the thirty Broch Tuarach men to the Frasers of Lovat. When he returns and shares his findings with Claire – the fates of several of the men on her list, but not all – she is excited to hear what he's found, but after they and Brianna have enjoyed a tea of cake and whisky, Claire makes an odd request to Roger while Brianna is out of the room: that he not take Brianna to the stone circle at Craigh na Dun, and that he not mention the name Jamie Fraser to Brianna.
That night, Roger is kept awake by Brianna's promise to do field research with him, so he decides to go through the Reverend's papers, believing this will help him fall asleep, for sure. Briefly distracted by the unwanted attention of Fiona, Roger finds an old newspaper clipping detailing Claire Randall's return in 1948, after having mysteriously disappeared three years before that. Roger recalls an offhand comment Claire made earlier about Brianna's age, and he realizes that not only did Claire reappear after being presumed dead, but she had also returned pregnant. Frank Randall was not Brianna's biological father.
Plagued the next day by speculation about what Claire might mean to do about revealing Brianna's true paternity, and whether the father, presumably a Scotsman, might still live in the area, Roger begins to wonder – and dread – what his role in the whole affair might ultimately be.
Roger takes Brianna for a tour of Culloden, where he tells her about the Duke of Cumberland and Bonnie Prince Charlie, and they share a walk across Culloden Moor, viewing the clan stones and the bits of heather left by visitors as tokens of remembrance. At the end of their day, Brianna asks if she can help with more of the dirty work of his research, adding on that maybe Claire will join them. Roger agrees to give Brianna more work to do, but privately prefers that Claire not join them, knowing now what he does about Claire's past.
Brianna comes alone the next day, though, and they get to work going through the Reverend's boxes upon boxes of stuff stored in the garage. They come across a box labeled "RANDALL", and Roger offers it to Brianna to take back to the bed and breakfast with her, to show Claire. Just before she leaves with it, though, Roger takes out one of the Reverend's journals, wondering why it was stuck in the box.
Later, when Roger has time to sit down and page through the journal, he reads the entries the Reverend made about Frank and Claire Randall in May 1948. The Reverend laments the hardship of Claire's return on both her and Frank, and gives spare details on visiting with them. The journal also references a request Frank makes to the Reverend before he takes Claire back to London with him: to find out about Jonathan Randall, Frank's ancestor, and James Fraser, both of the 18th century. The Reverend notes that he can't figure what these men of centuries past could have to do with the Randalls' current situation, and neither can Roger – quite. Although he knows about a Captain James Fraser, whom Claire had informed him definitely died at Culloden, Roger can't see what this could have to do with Brianna's parentage. One final entry from June 1948 intimates that the Reverend had found Jonathan Randall's grave at St. Kilda.
Roger invites Brianna and Claire to join him on a visit to St. Kilda; Roger told Brianna about Jonathan Randall's headstone being there, which Brianna holds off as a surprise for Claire. When they eventually find it, Claire is shocked. Her reaction disturbs Roger, as she seems to become angry, then resumes her composure as though closing off strong emotions she let loose so briefly. After Claire insists they go on ahead into the church while she sits in the shade of a tree, Roger shows Brianna the church building. Once inside and feeling intensely drawn to her, he impulsively kisses her. Roger tries to hold onto the feeling of the moment, but suddenly the silence is shattered by the sound of a woman's scream. They rush outside to find Claire, pale and appearing highly disturbed by something. Roger watches as Claire caresses the name and inscription on a headstone: "JAMES ALEXANDER MALCOLM MACKENZIE FRASER – BELOVED HUSBAND OF CLAIRE". Roger asks if she knows the name, and Claire tells them that she is Claire, James Fraser was her husband – and Brianna's father.
They take Claire back to the manse, where she rejects their offer of water and suggestion that she's taken ill from sun exposure. Claire begins to tell them about the stone circle on Craigh na Dun, and while Brianna still insists on getting help for Claire, Roger becomes cautiously interested in what she has to say. Claire tells them about going through the stones, meeting Jamie and the band of Highlanders, men of the MacKenzies of Leoch; she explains that she married Jamie to escape Black Jack Randall, but ended up falling in love with Jamie, and when she had the opportunity to return to her own time, she couldn't bring herself to leave him; how Jamie had fallen back into Randall's clutches during their brief time at Lallybroch, and she'd saved him from hanging to death, but not before Randall had had his way with Jamie; how they had escaped to France, and traveled to Paris to try and dissuade Charles Stuart of his doomed plans for restoring the Catholic king to the throne. She tells them the whole story of their time in Paris, then later back in Scotland, how they failed to prevent the Rising and how Jamie had sent her back through the stones, to protect her and their unborn child from imminent destruction on the eve of the battle.
Upon finishing her incredible story, Claire doesn't have to wait long for a reaction from her audience: Brianna, enraged that her mother would spin such a tale on top of telling her that Frank Randall wasn't her real father, throws a fire iron through a window. Roger, however, remains thoughtfully quiet after Brianna storms out. He wants to believe, but hasn't quite got there yet. He asks to see Claire's wedding ring, the silver one with the Highland interlace pattern, and at his request she takes it off for the first time in twenty years. They are both stunned to see a tiny phrase engraved on the inside of the ring: Da mi basia mille – "Give me a thousand kisses". It is Claire's patently shocked reaction that seals the deal for Roger; he believes her.
After Roger tells Claire what became of the various Jacobite players she had known in the eighteenth century, they go for a walk and philosophize about changing the course of history, and the relics that remain hundreds of years later. When they return to the manse, Claire broaches an unexpected subject with Roger: Geillis Duncan, who had borne an illegitimate son by Dougal MacKenzie, is Roger's ancestor, and Claire believes she hasn't yet traveled back into the past. She explains that she felt compelled to tell Roger, so that he might decide what to do: should he find Geillis, and warn her that she would meet her death in the past, or would doing so effectively erase Roger's very existence?
Roger decides to look for Geillis, or Gillian Edgars as she is known by in 1968. He and Claire visit Gillian's home, but find only an irritable husband who refuses to talk to them, and so they move on to the Institute for the Study of Highland Folklore and Antiquities, where Gillian attended classes. They learn about Gillian's personality from the director of the Institute, who uses the words "intense" and "obsessive" to describe her interest in standing stone circles.
That night, Roger takes Brianna out for dinner and then back to the Edgars' house, testing Claire's suggestion that perhaps Greg Edgars might convince Brianna of the truth to Claire's story. As Roger draws information out of Edgars about Gillian's activities and whereabouts, Brianna begins to suspect that he's up to something. After they leave, she confronts him, and he tells her about Geillis/Gillian being his ancestor. While Brianna is still reluctant to entertain the main points of her mother's story, she agrees to think about Roger's situation, for his sake.
After Claire returns from the Institute, from which she stole Gillian Edgars' notebook, the three decide to go Craigh na Dun on the eve of Beltane, believing that Gillian would choose that night to make her journey to the past. They climb the hill to find Gillian there just as a huge fire ignites, blinding them as Claire cries Gillian's name. Fearing pursuit, Gillian hurries toward the cleft stone, and vanishes through it. Roger, Brianna and Claire all experience the terrible effect of the stones on those that can hear them, the stink of petrol and roasting human remains thick in the air. As Roger comes to, he finds Brianna beside him, weeping with the aftershocks of terror. They panic for a moment looking for Claire, but they find her, lying insensible in the grass nearby. Roger carries her back to the car, and Brianna drives them back to the manse.
When Claire comes to, Brianna, knowing what the answer will be, asks if her story was really true, and Roger thinks of the Bible verse: "Blessed are those who have not seen, and have believed."
The following evening, Roger comes to a decision about something, and tells Claire that he has found something. He proceeds to read a passage in a book that describes one officer of the Fraser of Lovat's regiment who escaped the slaughter after the battle at Culloden, and states his belief that that man was Jamie Fraser.