Through A Glass, Darkly; opens on Claire waking up at the foot of the standing stones. Frantically she searches the tall grass around her until she finds a ring with a stone missing from it. The sight of this missing stone causes Claire to scream out in emotional agony before picking herself up and walking towards Inverness. She’s met on the paved road by a man in a car who asks her if she needs help. Claire appears stunned and then finally asks the man what year it is. He tells her 1948 and in her devastation asks him who won the Battle of Culloden. The man is stunned by her question and Claire grabs at him asking again. He tells her the British won and Claire crumbles in the road crying out in agony saying they are all gone.
Frank is called to the hospital in Inverness by a doctor who is treating Claire. Frank looks appropriately nervous but also rather excited. The doctor tells Frank that Claire is in good health and appears to have only a few cuts and bruises but emotionally she… well she’s better now.
Frank enters Claire’s room where a radio is playing as Claire gazes out the window at busy streets. Claire, not realizing who has entered, asks them to turn the “bloody thing off”. Frank obliges and then walks further into the room. Claire comments about how noisy it is and then catches a glimpse of Frank in the reflection of the window.
Claire is shocked to see Frank but states she’s back. Frank is glad she’s back and when he approaches her Claire gets a flash of Jack Randall and flinches. Claire apologizes and a camera man for the newspaper calls out to her and snaps a picture when she turns to look. A nurse ushers him away and Frank kneels down beside Claire’s bed. He tells her that Rev. Wakefield has prepared rooms for them while she heals. Claire wants to see Mrs. Graham and wonders if she still works for the Reverend. Frank assumes she still does and Claire looks at her 18th century clothing drawing Frank’s eye. He examines them more closely and is clearly baffled.
At Rev. Wakefield’s, the Reverend is watching Claire who is sitting outside reading through reference books about the Jacobites. Frank tells the Reverend that he received an answer from his friend Professor Atkins. Professor Atkins note states that Claire’s clothing is authentic 18th century Scottish woman’s wardrobe and is extremely valuable. Both Frank and the Reverend are stumped as to where Claire would have acquired such clothing.
The Reverend points out Claire’s sudden interest in Scottish history and Frank comments that she wasn’t interested before. Rev. Wakefield asks if Claire has given any answers as to where she’s been and Frank believes she will in time. But the Reverend points out the newspapers are also asking questions.
Out in the Reverend’s garden, Claire is wondering if there is a compete recounting of the Battle of Culloden but Mrs. Graham assures her that if such a thing existed the Reverend would have it. Claire becomes annoyed by the military planes flying overhead and Mrs. Graham tells her there is a possibility of war with Russia. Claire tells her “there is always another fucking war,” and then recounts how Jamie didn’t know what the word meant and how they’d laughed over her calling him a fucking sadist.
Mrs. Graham tells Claire whenever she talks about Jamie she mentions his sense of humor, his smile and his hair. Claire reminders herself Jamie is dead. Claire just wants confirmation that it is true and Mrs. Graham tells her that Jamie gave his word and asks if she has reason to doubt him. Claire doesn’t and Mrs. Graham tells Claire to tuck her love for Jamie away inside her and remember there is a flesh and blood man who still loves her. Claire looks towards the house to see Frank watching her.
That night, Frank goes upstairs, stopping briefly outside of Claire’s room before going to his own. He’s about to enter when Claire emerges from her own room and asks if he’d like to talk.
In front of the fire, Frank reminisces about their last night together and Claire tells him she remembers because it was there last night together. Claire tells him she wants to tell him what happened to her though Frank is quick to tell her he doesn’t have to know. Claire feels she musts but asks that he let her tell him the whole story and ask questions at the end.
Claire reminds him about how she went back to Craig na dun for the flower she’d seen. The screen fades to black and opens to Frank putting wood on the fire. It is morning and Frank stretches as he crosses the room. Claire knows her story sounds like she’s gone mad. Frank examines Claire’s 18th century clothing and tells her it is quite the leap of faith but that he believes her.
Claire believes his rational academic brain of his is telling him that his ex-wife has lost her mind. Frank wonders and why she says ex-wife and Claire tells him she married another man. Frank points out that she still wears their wedding ring. Frank admits her story is hard to believe but all he cares about is she’s returned. She tries to get him to understand she loved Jamie for two years. Frank tells her he understands but she doesn’t understand how much it hurt when she disappeared. He wanted to believe she ran away with another man so he could hate her but couldn’t bring himself to believe it. He believed whatever took her from him was something she didn’t chose.
Frank tells Claire he can’t understand her feelings for Jamie but he can accept them and that the loss of Jamie broke her heart. Claire tells him he doesn’t understand and Frank reminder her nothing she could do would ever make him stop loving her. Frank tells her they are still married and can still have a life together.
Claire drops the bomb that she’s pregnant and for a moment Frank is overjoyed and wondering how it is possible. Claire says the baby is Jamie’s and a stunned Frank goes from joy to angry rising above her with his fist clinched. He hovers a moment before turning and fleeing the room leaving a startled Claire behind.
Frank passes Mrs. Graham below and retreats to the garage where he smashes everything he can before crumpling to the floor in pain and disbelief.
In the manse, Frank apologizes to the Reverend about the mess. The Reverend skips over that and wonders about if Frank wants to have children. Frank tells him about the trouble conceiving and stays he had an exam and was told he is sterile. Frank tells him that it didn’t matter when Claire was gone but when Claire told him about the baby he was overjoyed and happy but then he realized the truth. The Reverend tells Frank other men have faced this and that when Mary told Joseph he was face with a decision. Frank becomes upset and tells him they are not Mary and Joseph and that Claire was fucking another man.
The Reverend looks over Frank shoulder to Roger who has come in to ask if he can go outside and play. He tells Roger to keep his breeches out of the dirt or Mrs. Graham will be on a war path. Roger says, “Yes, Father.” making the Reverend smile. Roger runs off and Frank apologizes. Frank comments about Roger calling him father. The Reverend tells Frank children see the world as it is presented to them. Roger knows he’s not his father but it is how he sees the Reverend and the Reverend has just decided to stop correcting him.
Frank doesn’t want to hear Claire’s baby is God’s plan. But the Reverend tells him that a child without a father and a father without a child brought together seems like God’s plan.
Upstairs, Claire asks if they are just to pick up where they left off. Frank says that he’s been offered a post at Harvard and he’s thinking of taking it now so they can get away from the British press. Frank then tells her he has conditions. He wants to raise the baby as their own not with a ghost. His other condition is while he’s alive he can’t share her with Jamie. She needs to stop searching for him and let Jamie go. Claire tells him she promised Jamie she would let him go so she’s going too.
She accepts Frank’s conditions and he hugs her telling her he hopes in time he can make her as happy as he is. She goes to her 18th century clothing and hands it to Frank telling him it is time to leave the past behind. She goes to take off Jamie’s ring but struggles with doing so and Frank tells her it is all right and to take it off when she’s ready.
Later Claire is packing and she puts the stone-less ring in her bag and then stands before the mirror in her modern clothing. She hears a sound outside and looks down into the yard where Frank is burning her old clothing.
Next we see Claire on a plane which has just arrived in Boston. Frank and she are exiting the plan and Claire stops to take in the city. Frank tells her just one more step and reaches out to her. Claire takes reaches out to take his hand…
… And back in the 1745 she takes Jamie’s hand as she comes off the ship onto the docks. Claire comments about Jamie being seasick and Murtagh tells them it stinks of frogs meaning the French. Murtagh gets the baggage being tossed off the ship as Jamie and Claire walk together.
That night in there lodgings, Jamie painfully lays out on the bed commenting it isn’t moving. He then tells her sometimes he feels Randall’s touch like he’s there. Claire assures him she’s there and she’s not going away. Jamie tells her she’s hard to get rid of and she says she’s stubborn like her husband.
Claire wants to talk about stopping the Rising and Jamie wonders if they can just make the Scots win but Claire doesn’t know enough to do that though Jamie wonders what she does know. She says she knows the Scots win some battles in the beginning and Jamie pounces on that wondering if they can just improve upon those wins. Claire tells him she knows nothing of the strategy or tactics. She doesn’t know why they won but she does know that they will end up on Culloden Moor and will lose and then the Highland culture will be wiped out. It is a better plan to infiltrate the Jacobite movement and disrupt their plans.
Feeling a bit of self-pity, Jamie says she has a high opinion of what a crippled hand and an Englishwoman can accomplish. Claire baits him by asking him since when wasn’t he up for a challenge. Claire points out that Jamie’s cousin Jared lives in Paris and he can vouch for them and make introductions.
Jamie says it isn’t an honorable path she lies out for them but Claire tells him it is about saving tens of thousands of lives and Scotland herself. Claire tells Jamie he has to trust in them and he says he does. He goes to kiss her but thinks twice about it and kisses her hand.
Jamie gets up and tells Claire he will write to Jared but then asks what they will tell Murtagh.
Next day on the docks, Murtagh is upset that Jamie and Claire are keeping something vital from him. They keep telling him they are trying to save Scotland but he hints at Claire secret and says they are hiding it from him. Murtagh has clearly gotten close with Claire as well and is hurt by her secrecy. Jamie vows to someday tell Murtagh at the proper time. When Murtagh walks away, Claire asks when the proper time will be and Jamie tells her to tell him since she’s the one from the future.
In the meeting with Jared, Jared wants to know what has made Jamie want to be counted among the Jacobite ranks. Jamie removes his shirt with Claire’s help and shows Jared his back telling Jared it is curtesy of the British Army. Jamie asks if there is a further reason to rise up against a King who would let such horrors be carried out in his name. Jamie tells Jared he wants to meet the Jacobite leaders, hear their plans, and carry them out. Jared wants to know why they should meet with Jamie and Jamie points out he’s a laird and the Jacobite’s could have the support of the Frasers. Jared is willing to think about it.
In the meantime, Jared wants Jamie to run his wine business while he’s out of town. Jared says they will also have the run of his house. Jamie wants 35% of the profits and Jared’s help which Jared agrees to saying Jamie will do fine.
While Jamie inspected Jared’s shipment, Claire went for a walk to get air and notices a sick man being taken off a ship. She see bumps on the man and follows. Jamie calls out to her but she doesn’t listen and Jared and Jamie follow her.
The man was taken to a warehouse where Claire has pushed her way in. She’s inspecting the man when Jamie and Jared enter. She tells them not to come closer and that she can’t catch what it is. Jared tells Jamie this is going to be trouble. The Comte St. Germain comes in.
Claire tells the Port Official that it is smallpox and the ship Captain gets upset with Claire. Jamie prevents him from hurting her and she tells the official the man is dead.
The Official tells the public it is smallpox and the Comte tells the Port Official it can be kept quiet but the man says it is too late. Claire asks for a quarantine and the Captain gets upset again backing off only when Jamie moves towards him. Jamie tells Claire it is best left to the port authorities.
The Port Official informs the Comte it is too late to keep this quiet and his ship and cargo will be destroyed.
Jamie tells Claire there is nothing more she can do and they go to leave but the Comte stops them asking her name. Claire gives it and the Comte tells her only an English woman would be so ill-bred and vulgar. Jamie warns the Comte to watch what he says to Lady Broch Turach and the Comte is not impressed. Jared tells the Comte that Jamie is his cousin.
The Comte asks if Claire knows what she has done and she tells him she’s done nothing but tell the truth that those men had smallpox. She has prevented the disease from spreading throughout the city. He tells her his cargo and ship will be destroyed and she will pay a price for it.
Later Jamie, Claire, Murtagh and Jared watch the Patagonia burn in the harbor and Jared says the Comte won’t forget and they’ve made and enemy. Jamie comments to Claire, another country another enemy, life isn’t dull with her. She says she will try to be more dull and Jamie says he wouldn’t change her to save the world.
They go to the carriage to leave and the Comte watches them as his ship burns.