The series begins with Mary arriving in France to meet Prince Francis, her betrothed since childhood. Scared, Mary is relieved to see that she might actually like her future husband. He greets her and escorts her to the castle. Later, while she is walking around the castle, Mary sees Francis making knives and swords. He tells her that he wants to have his own skill, something that he is good at. Mary charms Francis with her own accomplishments, that she can milk a goat and cut peat. Good skills to know, Francis allows, in case there’s ever an uprising in France they’d have to do something to get by. She is quick to respond that she’d take him back to Scotland and he could rule with her there. Francis hopes he’ll never have to take Mary up on that. Later, she brings him some pebbles but he tells her she should have announced herself and she begins to question if he is with someone. He then replies that husbands shouldn't have to answer to their wives. At the wedding ceremony, Francis watches her dance with her friends and they both begin to have flashbacks of their childhood.
Francis is all about keeping Mary at arm's length. Francis knows that political marriages can be called off at any moment and doesn't want to get too emotionally involved. However, he is attracted to her. Francis is firm in his belief that an alliance with Scotland would hurt France, and plans on dragging out their engagement for as long as possible.
Francis confronts her the next day wanting to know what Colin was doing in her room. He accuses her of intentionally trying to marr her reputation by getting back at him by sleeping with Colin. Mary, of course, denies it and tells him to leave it alone because Colin is dead. She then reminds him that they may not even be getting married and that he doesn’t even want to. After a heated discussion the two almost kiss before Francis turns away.
In Snakes in the Garden, In the presence chamber, Queen Catherine is telling her youngest son, Charles, about his intended bride. When it’s mentioned that his young bride, Madeleine who is only seven, is nervous about the journey to meet her, Mary volunteers to go since she thinks she’ll be able to reassure her given that she, too, was sent away from her family as a child. Queen Catherine and Nostradamus agrees, and Mary is sent on her way with Francis and Charles. Later, Francis saves Mary from Simon Westbrook when he threatens her, convincing the shaken sovereign to act as if their relationship was more solid then rumors made it appear. “Can you do this?” He asks Mary, extending her hand. “Absolutely.” She replies. The next day, Mary and Francis are watching Charlie and Madeleine play a game and they begin to remember the past as Francis says she was always impatient with him. She then tells him that she thinks his mother is plotting against her.
Later, Francis, who has joined Mary, determines that the assassin must have absconded with the body of the dead woman, and sends the guards to search the castle and the grounds. Mary wonders if the assassin could have left through the passage in her room, and shows Francis the door she discovered. He says that he doesn't think so, since most of the passageways are dead ends since the castle has been built up, but says he’ll have the guards check them anyway. Then Francis chose to defend Mary and look out for her and he actually threatened his mother if she continued her quest to destroy Mary.
He wants to keep Mary safe, not simply because his family is tasked with protecting her, but because he cares about her far more than he’s willing to admit. He commits himself to Mary and adds that they should at least try to start out as friends, and Mary happily agrees.
In Kissed, Mary tries to convince King Henry to send six companies from France to Scotland, but he doesn't think it prudent for France were he to lose those men. Francis agrees with Mary, but he feels as though he doesn't have any real power yet. Later she meets Tomás whom is apparently taken with her bold behavior and ultimately proposes marriage to her, swearing that his father, king of Portugal, is fighting to make him legitimate since he's his only son. Mary is hesitant to accept his proposal because of her feelings for Francis, but Tomás is promising to send six companies of men from Portugal to protect Scotland in exchange for the engagement.
Tomás also tries to win her over with a very sensual dance to "Portuguese music" at dinner that night causing Francis to become jealous. Mary ends up telling Francis that Tomás proposed. Francis does something to win Mary back. The prince resorts to blackmail in the form of the king’s obvious attraction to Kenna. King Henry is impressed with this low blow and agrees, finally, to send help to Scotland. Francis sends out his half-brother, Bash, to deliver the news and send the troops. Mary is thrilled by the news. Sadly, Bash gets injured by someone and returns on his frantic horse the next morning bleeding from the belly, French troops unsent. King Henry tells Francis that this is what happens when you follow your heart.
Francis chooses to let go of his emotions to avoid seeing any more people he cares about get hurt. Mary tries to comfort him outside the castle. The end result of the comforting is Francis kisses her — her first kiss. Francis then pulls away and tells her to marry Tomás, since he can’t help her. The kiss was a goodbye kiss and although Mary clearly doesn’t want to take Francis’ advice, she really doesn’t have much of a choice in the matter.
In Hearts and Minds, Mary and Francis grow closer amongst everything that happens. Mary accepted Tomas’ proposal in last week’s episode, Tomas and Francis have a archery competition as the court (especially Mary) looks on. Tomas ends up winning the competition and offers his favor – a rose – to Mary, who reluctantly accepts then rushes off to comfort Francis. As Mary discovers, Henry’s approval comes at steep costs. The King only found out about Westbrook’s deception because a prostitute named Judith overheard Westbrook boasting at a tavern, and came to warn him. In order for that woman’s testimony to hold up, however, someone needs to vouch for her – and that someone is Mary. The Queen of Scots agrees so that she can get out of her engagement to Francis.
Afterwards, Mary and Francis make plans to meet by the lakeside at sunset, not knowing that a Portuguese envoy has spied them embracing. Meanwhile, Francis stands by Bash’s bedside cursing Simon Westbrook’s name. His mother Catherine shows up to tell him it’s not his fault, but that he needs to let Mary go – but Francis refuses. His instincts were right before about the English, and now they’re telling him Tomas is bad news. Francis leaves to meet Mary by the lakeside. He tries to warn her about Tomas – there are rumors that he’s scheming and cruel to his servants – and that they need to make sure Tomas is held accountable for how he treats Mary. Mary is touched by his concern but tells him she’ll be fine. As she starts to make fun of him, he passionately kisses her.
At the costume ball, Mary questions Simon about the royal seal she found in her room, but is interrupted when Tomas shows up and demands Mary’s attention. Francis and Bash rescue Mary from Tomas’ claws and accuse him of being the spy. Tomas does what he does best and marches off in a huff, giving Francis and Mary time to make a plan: they need to gather witnesses to prove Tomas’ deception. Two of the people they need are Judith, the woman who pointed the finger at Westbrook, and Miguel, Tomas’ servant and whipping boy.
Later, Mary, Francis, and Bash to show up with both witnesses, and Westbrook gets to keep his head. Later that night, Francis pays a visit to Mary. Mary is a bit in awe over Francis killing someone to protect her. She’s impressed by his judgment in a lot of matters, from how he handled the Tomas situation to how he understood they couldn’t go too far during their secret make-out session. He says his heart is telling him to be with her regardless of the consequences, but she knows and respects that his head says differently. He thinks that she’s a great queen and she thinks he’ll make a great king.
In A Chill in the Air, Mary and Francis are on the best terms they've been on since Mary arrived at the castle, thanks to Scotland's borders being secured. Francis meets with Mary to “discuss where they’re at with one another.” Apparently where Francis is at, is declaring himself and his heart as belonging only to Mary and seal it with a kiss, just in time for the Harvest Festival that afternoon. Francis has made a boat for Mary that he’s named after her. Mary is touched. Then a man comes up to tell Francis they found a woman running along the edge of the forest in a fright, and that she asked for Francis – and then Olivia comes in, and Francis rushes to her side to comfort her. Bash takes the opportunity to sidle up and tell Mary all about Olivia and Francis’ old romance and that Olivia broke Francis' heart.
Afterwards Francis comes to Mary and tells her about his relationship with Olivia. His face when he says “there was an incident. In… the boathouse. An incident where we were found. In the boathouse.” With Mary’s support, Francis plans to help Olivia regain her credibility. That night, Mary asks Francis about his talk of marriage to Olivia, and he admits that in a moment of weakness he had considered it. However, as he reiterates, he has promised himself to Mary now and intends to keep that promise. To help him with that, Mary has arranged a suitable arrangement for Olivia in Paris.
Not two seconds later, because this is the type of day Mary is having, Francis comes and double confirms that Olivia is moving into the castle. Francis claims that the arrangement in Paris is no longer an option, and that he’s looking for another option but it’ll take some time. Mary realizes something has happened between Olivia and Francis. She tells him to make Olivia go away, only for Francis to tell her that “this is my court, and I’m the future King of France.” He also threatens to make Olivia his mistress, and Mary storms off chugging wine. Francis goes looking for her, and finds Bash and Mary kissing. Mary confesses to Francis her regrets, but Francis is cold to her. Their boats go down separate paths in the lake as Francis leaves Mary’s side to join Olivia.
In Chosen, Bash takes Mary and Francis aside to explain the blood debt that he owes the pagans and how he must either choose someone to die or have the woods dwellers choose someone, with their target looking to be Mary. Francis thinks that the pagans are just trying to get at Bash through Mary and while she pledges to do some digging around the castle to see if anyone saw a strange figure go into her room, Francis tells Bash that he doesn't blame him for cutting the bodies down. The reason that he's so upset is that there are too many secrets clinging to the castle walls these days. The next day, Mary is woken by a bleeding stag's head that someone strung up to her bed, the face of the dead animal looking her right in the eye. The way that those responsible were able to do their deed without being noticed by her by using poppy, which they put in the drinks of Mary and her guard. She also finds that she has the symbol from the necklace burned onto her hand, making Francis think that it might be dipped in some type of poison.
That night, Mary finds herself worried sick about Bash's whereabouts, a worry that only increases when she learns from Francis the reason why Bash took someone out with him. He wants to sacrifice this man for Mary and to ensure that the future Queen of France won't be in danger from the pagans, a gesture that shows just how deeply his feelings for her run. Francis uses this moment to confront Mary about seeing her kissing Bash; she tries to explain that she wasn't thinking clearly, but he comes down on her for navigating court with feeling and heart rather than intellect and savvy. Because of her, he argues, he doesn't know who Bash will be when he returns.
Bash returns from the woods in the morning and Francis tells his brother that if he would have died out there, that he would have deserved it, that he would have brought it on himself. He then informs Mary and Bash that the three of them are rulers and they need to start acting with the clear heads that they've been lacking lately due to the situation between the three of them. As such, anger can no longer divide them and while his engagement to Mary will remain, it's only in name; if their respective countries need something from the other, the agreement will be honored, but otherwise, they're to spend time apart. He gives her permission to spend time with others, only not Bash, and claims that he's doing all this to take control of the spiraling situation between them. Once the conversation is over, Francis goes to Olivia.
InLeft Behind, Mary is confronting Francis over his relationship with Olivia and how she feels like a nunnery of one watching him parade her all over court. He rationalizes that each of them could be married off tomorrow for business/alliance needs and that he needed to forget Mary for a while after what happened with Francis. Count Vincent of Naples arrives less than a year after Henry defeated Italy in a war. Vincent recounts the events of France's war with Italy to Mary, Francis, and Catherine, including the fact that he had to negotiate the release of his son Roberto and how hostages are an old tradition in the art of war. After eight months of maneuvering, he managed to secure Roberto's release for 1500 ducats, which he says taught him the value of life. However, the castle soon falls under siege and a stream of Italian soldiers pouring into every room of the castle in hopes of accounting for everyone.
Vincent claims to want ten times what he had to pay for Roberto from France, but instead, Catherine tries to give him Mary, telling the Count that she could bare him children and that she would be forced to accept marriage once he ruined her. However, Francis offers himself up as a hostage for the Count as a way of exacting revenge on Henry for taking Roberto, an offer that Vincent ultimately accepts. Mary and Catherine plot on how to go about defeating the Italians. Mary mentions the secret passageways under the castle and the hidden door in the hall that will take them there, which Catherine skeptically accepts as a reasonable escape attempt. She adds the element of distraction to the plan, though, by suggesting that they attend the feast and try to buy Francis as much time as they can. They'll keep Vincent and his men busy, giving Francis and the servants time to escape; Catherine says that she'll stay behind with Vincent to allow Mary and her ladies the chance to leave the castle, as well, claiming that she would go into hell for her son and that they can only trust one another right now. Knowing that Francis would not come back alive if he were to leave with Vincent, Mary agrees to the plan; Francis, though, remains skeptical, telling Mary that he doesn't want to leave without her and apologizing for everything that happened with Olivia. Mary responds by saying that she believes that Francis can help lead those in the castle to safety and the two kiss before a guard comes into the room.
Later, after being abandon by Olivia, Catherine grows noticeably tenser and threatens Vincent with the fact that Henry will go to war for his heirs. Vincent doesn't care, though, and she then offers Mary and her ladies to him and his men, claiming that they can take their virtues. The men swarm Mary, Kenna, Lola, and Aylee and just as the sands on the hourglass run out, Catherine tells him that the reason his son died was because his father was too cheap and had to spend months haggling for his release. Blood begins pouring from the nose and ears of each of Vincent's men and Catherine reveals that the gold she offered them at dinner was poisonous to the touch. Before he can attack the Queen, though, Mary stabs him with a knife and Francis comes in to cut off one of his hands therefore, killing him. Francis confesses to Mary that he loves her and that the two need to be together in order to stay sane. The two begin kissing and end up in bed, where they make love for the first time.
In Fated, It's the morning after Mary and Francis made love for the first time and they're decidedly closer than they were prior, with Francis wishing that Mary was already pregnant so their wedding can be pushed up. Their time gets cut short, though, when one of the servants comes into the room and informs Francis that a Cardinal was in the throne room and waiting for him. The papal emissary brings word to Henry and Catherine that the Tudor queen is dying, meaning that it's nearing time for the next Queen of England to assume her title. The next queen? Mary. As a marriage to Francis will help her cause, Henry proclaims that it's time for a marriage between his son and Mary, but during this, Nostradamus has a stronger vision of the death and destruction this marriage will bring, which includes Mary with blood on her hands.
Outside, Mary and Francis take a walk to get away from the madness of the castle and the pressure of Mary's decision about England. She's terrified at the prospect of starting a war and of no one supporting her in her cause, but Francis assures her that he'll be there every step of the way and that they now have time before anyone gets in the way of their love for one another. As such, he proposes marriage to her, claiming that they can figure out later what they'll do with England; he'll listen to her, pressure her, argue with her - whatever she needs. Mary says yes to the proposal and the two run off to the castle. Lola worries about Mary's safety, Mary assures her that Francis is a good man and that their wedding tomorrow will be a good thing for all involved. Then Aylee, Greer, and Lola begin to dream up how Mary will look on her wedding day. Catherine meets with Mary and questions her of her thoughts on Nostradamus' legitimacy before telling her of the dark prophecy of Francis' death. As his visions almost always come to pass, Catherine suggests that Mary walk away from Francis, causing Mary to recoil in surprise. She doesn't want to leave Francis and begins questioning the prophecy. She trusts that Mary won't use that against her and her desire to protect Francis is stronger than her desire to live. Catherine warns her to be very sure about her resistance to the prophecy and asks her to think of a prophecy of his that didn't come true, something she cannot do. Also a condition of the agreement? Don't tell Francis of the prophecy, as he'll try to talk her out of her fears and convince her that they can choose their own fate.
Mary goes to Nostradamus, proving that she at least somewhat believes in the prophecy, and he tells her the only way that the most recent prophecy can be changed is if she agrees to leave Francis. Every incarnation of the vision has his death tied to her hands - a Francis barely older than he is now, cold to Mary's touch.
In Francis' room, Francis dresses and tells Mary she should be happy because they’re getting married tonight. She says she thinks they’re testing fate by wanting too much. She says that Queens and Kings don’t get that much happiness. Francis says that they have devoted their lives to their countries and are taking risks all the time. He says they should do what’s right for their people. Mary says she likes the words “we” and “our.” Francis tells Mary he would die for her and they hear a scream. The two rush out to find that Aylee had fallen over the railing and hit her head, which was surrounded by a pool of blood. She reminds them Nostradamus said she would never go home again. She says I must go home now and dies in Mary’s hands.
Mary quickly packs her things, as she fully believes in Nostradamus' gift and doesn't want to risk the lives of anyone else she loves by ignoring his prophecy. Before she leaves, she goes to Henry and lays no claim to the throne of England; even though he claims she's risking everything she's waited so long for, she still walks away, though Francis catches up with her and tries to get her to stay. She says that she can't trust his claims of only wanting her, that "love is irrelevant for people like" them, and that she won't let anymore people die for her. Mary goes out to the stables where she tells Bash that she's going far away for the time being. He says that "away" is where he was going, too, and the two ride away from the castle, just as Francis comes running out after Mary, falling to his knees when he realizes he lost her.
Mary and Francis are reunited in For King and Country. But before Mary is returned to the French Court, Francis has been searching for her the past week. Queen Catherine tries to convince her son to give up his search, but she has no luck there. She persists in trying to talk him out of wanting to wed Mary, but that is also completely futile. Francis also thinks his mother had a hand in Mary leaving. When Mary returns, he tells her that if the search had escaped back to Scotland he would have gone there to see her. He doesn’t believe the reasons she gave for leaving him and wants the truth. He manages to get a snippet of it out of her; that it has to do with Aylee’s death. Someone approaches then to tell Mary the king wants to see her. In Mary’s chambers, Francis has come for a visit at Mary’s request. He’s heard about how Bash’s life is on the line and Mary still won’t marry him. Mary explains the prophecy then, and Francis is incredulous. He thinks its all ridiculous, and can’t believe Mary believes it. She does though, because of how Nostradamus predicted Aylee’s death. When Francis talks about telling his father Mary insists he not because it would get both Nostradamus and Catherine killed. When Francis seems angry with his mother Mary makes a point of mentioning that everything Catherine has done against her has been for love of him and she doesn’t deserve to die for that. Francis won’t believe the prophecy, and Mary won’t change her mind. Francis’ plan now is to try and get Nostradamus and Catherine to change their minds. Mary then forms a plan of her own.
Later she, informs Francis that she was not only not going to marry him, but had made a deal to have the King have Bash declared as legitimate and marry him instead. Not only is she saying she is going to marry Francis’ brother, but by having him legitimized means Queen Catherine, Francis, and his other brothers will be declared illegitimate and the Queen stripped of her title. Francis lists off everything that he, his mother, and his brothers who will lose everything because of this and says he won’t forgive Mary and Bash just because they think they’re protecting him.
Before Francis leaves the castle, he tells Mary that he clearly still thinks Mary’s wrong to believe the prophecy, but there seems to be a begrudging respect for how headstrong she is.
Francis and Mary are reunited in Consummation. They have their first conversation since he left the castle. He tells her that he's only here to get the matter of his mother's fate settled and that when that happens, he's going to leave and they're never going to see one another again. Nostradamus mentions to Catherine that the Clarissa's death took away the violent images of his vision about Francis' death. Since his vision was about Catherine's first born dying at the hands of Mary and he didn't know that Clarissa was the first born, he now sees Francis and Mary being happy together, married for years with a whole litter of children. Nostradamus urges her to save herself now that Francis is back at court and she hisses out that if she can't convince Francis to wed Mary, she will be watching him burn to death at the stake. Catherine reunites with Francis and begs him to go to Mary, citing that the prophecy had changed and that what matters is his love for her. If he gets back with her, he would save his mother's life and put himself in position to take the crown, so he rides out to the church to where Bash is and makes the first move to reconnect with Mary. Francis tells his brother that there need not be an elopement with Mary anymore and when Bash mentions that neither he nor Mary would trust the word of Catherine, Francis accuses him of playing on Mary's fears and the two begin tussling. Soon, Mary arrives and breaks them up, only to learn about the prophecy and how her fate is now her own. When Mary gets back to the castle, she confronts Catherine about the prophecy change and how she doesn't believe a word the queen says, only for Catherine to use a piece of jagged glass to cut her wrists. Terrified by the gesture, Mary heeds her warning to talk to Nostradamus about the prophecy alterations, except that she doesn't get a chance due to having to clean Catherine's wounds and Henry summoning them to the throne room. A messenger just came with the news that the English queen is dead. Mary has to put in her claim to the throne immediately and wed the next King of France that very night.
Meanwhile, Mary frets about having to make the choice between Bash and Francis, only to have Catherine arrive with what she claims is the letter from the Vatican about Bash's legitimization. Mary takes a look at the letter and goes to Bash, where she informs him that while she may love him, she loves Francis more and that is who she will marry. She then finds Francis in the hallway and the two embrace before she shows him that Catherine gave her a blank paper, allowing her the decision on who to marry rather than letting Henry force her into one option or the other. Mary tells him that it's always been him and he agrees to marry her and protect Bash from the impending danger that will surround him now that he has made a play for the crown. The wedding takes place, Francis and Mary are finally wed, with the episode paralleling the pilot episode. In the first episode of the series when Francis' sister got married and the show foreshadowed what it would be like for Mary on her wedding day. In a note to that episode, feathers fall from above as Francis and Mary enter the reception. It was a homage to Francis watching Mary dancing in episode one and the flashback to her and Francis as children when they burst open pillows and had feathers flying everywhere.
Following the reception is the consummation, where several key figures around the castle watch as Mary and Francis make love. Also in attendance is Bash, who was stopped from leaving the castle by Henry and made to watch so that he knows what isn't his.
In Dirty Laundry, they are coming back from their honeymoon. In the carriage, they talk about going back to politics, betrayals and backstabbing together with going back to the French Court, where, when they arrive, are warmly welcomed back. Later, Mary hears about Lola's pregnancy and figures out it is Francis' child. She is clearly hurt by this truth, though she hides that. At the end of the episode, she is in bed with Francis, probably after making love. She watches him sleep, sadness being read in her eyes.
In The Darkness, Francis finally tells Mary about his affair with Lola, unknowing that Mary already knew. He thanks her for being understanding and mercifully and asks if Lola has told her already. Mary denies that, lying to him. Soon after, Mary goes to Lola telling her she is afraid for her marriage and that she might lose Francis' trust if truth comes out. They also talk at the First Light party, Francis revealing that Philip Nadine, Lola's possible suitor, prefers men. Later, Mary enters Francis' chambers and sees lit candles prepared by Francis for her. He wishes to spend the night with her, however she is reluctant. Francis confesses that he wants babies only because he loves her, and doesn't love her only because he wants babies. Though still reluctant at first, she finally agrees and Francis starts undressing her. The camera cuts off with Mary moaning as he undressed her.
In Monsters, Francis tells Mary about the Queen of the Bean celebration. Mary doesn’t remember it, since Catherine tried to keep the children away from such things. Once a year all the female servants of the castle have a chance to become queen for one day, as long as they find the bean in their slice of cake. Henry invites the winner into his bed as long as she is pretty. Francis never liked the tradition, especially when Diane was at Court, since his father would have to juggle several women on that day. He begins to tell Mary that he and Bash would leave the castle, going on a hunt. Mary tells Francis that is it ok to miss his brother. The only good thing Mary can find about the contest is it will give the inhabitants of the castle something else to discuss, instead of her apparent lack of heirs. Francis jokes that he will start pestering her about it instead. Kenna approaches Mary and Francis outside of the throne room, telling her that Greer is ready to introduce him to Mary. Francis questions the introduction, and Mary explains that Greer’s fiance arrived in Court a few days prior.
Bash arrives at the castle for help in order to rid of the Darkness. Francis believes that Bash came back to win Mary’s hand and warns her not to let him get close to her again. Mary goes to see Bash, informing him that she got him a ship to Spain. He refuses the offer and she yells at him, telling him it was a mistake for him to come back to Court and that several people want him dead. He thinks the only person is Francis and she tells him that he did not try to have Bash murdered but admits that Francis could. Bash ignites a bitter jealousy in Francis, making him a person that Mary barely recognizes. Bash thinks it is because Francis know Mary could have been happy without him, happy with Bash. Mary tells Bash that there is nothing between them and she is only worried about his welfare.
Francis finds Mary and Bash leaving the dungeon cell. He says he came down to check on Bash, since he was worried about him, but instead finds him with his wife. Mary tries to tell Francis that Bash did not come for Mary. Bash agrees saying he came for the castle resources, to find someone in the woods. Bash tells them that he saw it himself, when Francis doesn’t believe him, and that someone else (Olivia) can corroborate his story. Francis and Mary meet Olivia. She makes Francis believe that there exists a monster in the woods, which according to Nostradamus is a human. Francis is convinced that Bash is telling the truth and decides to eliminate the monster. Mary reminds them both Francis and Bash to know who their enemy is.
Sometime after both Francis and Bash return to the castle, Francis attempts to go speak to his father (whom has gone mad) but Mary warns that he is not well. Francis knows, afraid that Bash’s head was going to come off earlier. They both then attend Sebastian and Kenna's Wedding.
Mary and Francis' duties as rulers comes into play in Liege Lord. Mary gets some very unwelcome news this week – there’s a secret clause in her alliance gives Scotland to France if she dies without producing an heir. She informs Francis and they devise a plan to force their parents to break the contract by leaking the information to the Scottish protestants. Catherine has Mary’s chosen messenger, Lord McKenzie, and his men slaughtered before they can go back. Upon hearing the news, Francis comforts Mary as she cries. Mary then threatens to spread the news about Henry’s mental state to ambitious noblemen if Catherine doesn't burn the contract. Catherine tells her it will case civil war. Mary says that she is the Queen of Scotland, not France and says she can take Francis with her to Scotland to serve as her consort. Mary says she has sent three riders and unless she sends word saying not to, they will release the news to influential men and the Vatican. Catherine asks Francis if she’s bluffing and Francis backs his wife up. Catherine hands over the original with Mary’s signature and Mary tells her to burn it and she does.
At the end of the episode, Francis tells Mary it was a great bluff and she tells him that she did send the three riders. He’s shocked because it could have destroyed France. She tells him she will be Queen of France one day but says Scotland only has her to look out for its welfare. She tells him she will always choose her own country over his and caresses his cheek.
Francis and Mary's relationship is tested in No Exit. James tells Mary that too many of the powerful people in Scotland are French. He wants her to come home with him so the Scots can see they have a Scottish Queen. Mary discusses the matter with Francis, but his first suggestion is to send more French diplomats. Mary recognizes this as counter-productive. He doesn't want her to go, though, because he needs her to finish negotiating with the Cardinal and they’re trying to have a baby – an heir for France. Mary has already told him she won’t put French interests before Scottish interests so she gets mad. Francis later talks the matter over with Bash during sword-fight practice. He wonders what he should do when he has to choose between being a good king and a good husband. Bash tells him to be a bad king, and Francis recognizes that that’s why Mary wanted to marry him. It’s not that simple for Francis though. Still, he follows his brother’s advice and tells Mary he’ll go with her to Scotland.
The matter isn't settled, though. Francis sees one of James’ servants paying for an expensive prostitute with English money. He questions the man about it, and shows the money to Mary. He reminds her that her brother is Protestant and asks if she can really trust him. Francis resorts to having the footman tortured to get more concrete answers and finds out that he was paid to murder Mary by the English, who want James on the Scottish throne. Francis tries to convince Mary not go with him, but Mary trusts her brother. She says he’s written to warn her about a lot of threats that would have benefited him. Francis refuses to accept her decision and has her locked in the tower. She tells him that if Scotland falls, she will never forgive him.
A month after Francis locked Mary in the tower she is able to speak to him without screaming in Toy Soldiers. He wins her back largely through helping with the Protestant rebellion taking place in Scotland, the one Mary’s brother warned her was on the horizon. Mary needs to send an army to defend her mother and Francis makes a deal with her uncle, the duke of Guise, to get it. However, Henry gets France into a battle their own forces cannot win so Francis changes his mind and uses that army to retake Callet from the English. Before Francis goes into battle, Mary makes him promise her two things: Stop making promises he can't keep and to come back to her. At the end of the episode, Mary can forgive him for doing what France needs him to but it means she’ll have to take measures to save Scotland that he might not like.
Mary and Francis are reunited in Long Live The King, Francis and the Duke of Guise return to French Court, victorious over the English at Calais, returning the French port to French control. Francis mentions winning alongside courageous men and the Duke, but fails to mention his father. Catherine notices this slight, hoping Francis would say something. He becomes distracted when he sees Mary, going to her and greeting her with a kiss. Her uncle mentions Henry’s part in winning back Calais, which paves the way for Henry’s announcement. Hurrying to their room, Mary and Francis take their time undressing one another in their rooms. He thought she wouldn’t forgive him for taking the army to Calais instead of to her mother’s aide. She informs him that her mother escaped and is fine. Francis was worried he wouldn’t be able to tell Mary that he loves her again. In bed, she tells him that her mother managed to escape Scotland and that her brother is now in charge there. Mary and Francis discuss that she has a small window to stake her claim on England. Elizabeth has not yet solidified her role, having not been coronated yet. Mary wants everything to just go away and to be able to just love Francis. She questions if he will still support her, and then tells him that she is thinking of writing to Elizabeth.
Francis cannot believe his mother when she tells him that Henry intends to sail for England by the end of the week. He knows that their army has been depleted and going to war with the English now will destroy them. Catherine thinks the only thing they can do is murder Henry, but Francis refuses. He wants some time to try to get through to Henry, saying he will not give up until all options have been taken. Mary promises him time, but begs him to hurry. When he leaves, Catherine thinks they need to take matters into their hands. She knows Mary would be betraying her husband but Catherine would be doing so much more. And she is willing to relinquish her crown to Mary when Francis becomes king because it is the right thing to do. Catherine and Mary will plan the murder of Henry, keeping Francis out of it.
Francis returns from his hunting trip with his father. He says he convinced Henry not to invade England and that he believes his father is getting better. Mary is afraid it is too late. Francis tries to reason with Catherine and Mary, the three of them discussing Henry’s imminent death. However Catherine and Mary's plan fails. Later, Francis and Mary argue about the decisions that Mary made. She tells him she was doing it for the good of France, a country Francis himself put before her in the past, and she wanted to spare Francis of carrying that burden with him for the rest of his life. He is upset because he stood by her when she decided not to go after England and he thought she stood by him. He wonders who she is turning into.
Going into the season finale, Francis realizes that any hope for his father is long gone. He later laments this fact with Mary and Catherine. They conclude that it’s too late for an assassination and a superior force must remove him from court. Mary notes that perhaps the army generals that Henry dismissed before the battle of Calais may feel betrayed and will fight for their cause. With Henry's death, Francis will become the new King of France. When Mary learns from Catherine that Henry plans to kill Francis, she goes to desperate lengths to protect her husband. Later, Henry is killed by his own son, Francis, in the joust and Francis becomes King. Both Mary and Francis become the new rulers; King and Queen of Scotland and France.
By the end of the episode, Mary opened up to Francis telling him she is afraid of the changes happened to her, she feels herself growing harder. Eaten up by the guilt Francis was ready to confess his great sin to Mary but was interrupted by the message of Lola is having the baby. Mary confessed Francis the truth about Lola carrying his baby, she eventually even pushed him to go after her but changed her mind upon hearing the Plague infested France. But Francis had to do the right thing, he left the castle anyway inserting a wedge between him and Mary who lowered the gate behind him.