At Mary's arrival, Francis is walking out fast to greet her but pauses in a moment so fast but it is apparent that her beauty has fixated him. Later, Francis is seen making knives and swords. He tells Mary 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 for fire. 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 with her. Francis hopes he’ll never have to take Mary up on that. Mary comes to see him again then realizes he's with someone and learns of Francis' straying ways.
After Francis' sister's wedding, Mary and the girls begin dancing and having fun which causes Francis to watch her. Bash and Mary share an intense look that Francis catches. Then feathers rain down and spark a memory for both Francis and Mary of jumping on a bed as children and feathers exploding from the pillows. They remember the good times they shared and are about to dance together before the bedding ceremony begins and interrupts their thoughts.
Later, Francis confronts Mary about his concern for his country outweighing his happy memories of playing with Mary as children. He believes an alliance with Scotland could ruin France and doesn't want to jump into a marriage with Mary yet. Mary, however, is more concerned about Francis' feelings about her. She begins to ask him if he would want her if they weren't royals, and there was no stake in their marriage. He almost kisses her but he refuses to get caught up in love.
In Snakes in the Garden, Francis, who tells Mary they must play up their romance for the sake of the Englishmen at court, so they’re none the wiser of just how weak the French-Scottish alliance truly is. The next day, Mary and Francis are watching Charlie and Madeleine play a game and Mary tells Francis just what his mother is up to. Francis' immediate inclination is to distrust Mary’s suspicions, since he can’t imagine his mother trying to have Mary killed. Francis has a certain inherent faith in his family, and in the honor of the royal station, such that he can’t conceive that Mary would come to harm while under their protection, much less from those tasked with protecting 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 passageaways are dead ends since the castle has been built up, but says he’ll have the guards check them anyway.
Francis later confronts his father, demanding to know whether they are planning to let Mary go or if they are going to have him eventually marry her. The King says that Mary isn’t safe in England, and isn’t wanted in Scotland unless she comes back with a husband and so she shall stay put in France, waiting for The King to determine whether or not he wants her to marry his son. Francis is highly irritated by this news, and says that it’s completely unfair to Mary and that she is a girl, not just a pawn. When Francis goes to see Mary, she holds his hand and thanks him.
Outside, Francis has caught up with Bash who has found Colin hanging from the tree. Bash guesses it’s the French guards who have caught up with Bash, but Francis reminds him that their guards wouldn’t hang a prisoner that way. As they begin to attempt to cut Colin’s body down from the tree they hear a rustling in the woods. Bash demands to know who’s there, and then speaks in an unknown language. Later, Francis stands up to his mother and gives her a warning about trying to murder Mary.
The next day, Francis promises 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, Francis tries to get his father to send troops over to Scotland to help the Scottish defend themselves from the English, who have just sent a bunch of men to the Scottish-English border and are obviously looking to start a fight. Francis has no luck getting his father to agree to send troops to aid Scotland, and Mary, who is desperate for aid for her country, has just been proposed to by Tomás, the bastard son of the king of Portugal and who might be decreed legitimate by the pope in the coming days and become next in line for the throne of Portugal, and she is considering his proposal, even though she loves Francis and wants to marry him, because he has offered to send troops to Scotland if she agreed to marry him.
Tomás' marriage proposal to Mary makes Francis fight even harder towards convincing his father to send men to Scotland. Francis realizes how to convince his father to aid Scotland when he sees Kenna look at the king after she ran up to him and was rejected- Francis was going to black mail the king, his father. Francis approached the king and told him it would be a shame if Francis' mother, the queen, and the king's mistress found out that the king had another mistress, since there is already enough tension and jealousy between his wife and first mistress already. Francis then tells his father that if he sends troops to Scotland's aid then he won't tell the women about his new mistress. The King agrees and states that he is proud of Francis for thinking like and acting like a king. The king then tells Francis that he will need to send the best rider in order to get there in time, and the best rider it turns out is Bash.
Francis then sends Bash off; but Bash comes back near the end of the episode with a sever stab wound and is near death. Francis feels guilty for having put his brother in harms way because he had let his emotions for Mary cloud his judgment. Mary then approaches Francis and tells him he did the right thing. Francis and Mary then kiss. However, Francis then tells her that she should agree to Tomás' marriage proposal and help out her country.
In Hearts and Minds, Francis and Tomas engaged in an archery contest. On the field, Tomas does a bit of showboating and Francis does his best to be polite. Tomas wins the competition and Tomas offers Mary a flower. She takes it because it would be rude not to, but it probably comes off as rude anyways to the crowd who think she’s there as Francis’ fiancé. Mary goes up to Francis later to apologize, and he states that he’s pretty sure it was a calculated move on Tomas’ part rather than an error in etiquette. Mary also tries to tell Francis that she wishes she could stay, but he cuts her off because hearing it wouldn’t make him feel better. He regrets that, were it not for Bash being ambushed, Mary wouldn’t have to go. The King gets a message and stands, drawing everyone’s attention. He accuses Simon who was trying to intimidate Mary of being the spy who caused the ambush against Bash and their men and has him apprehended.
In Bash’s room, Francis watches over his injured brother and his mother comes in to talk to him. Catherine worries that Francis is blaming himself for what happened to Bash, but he’s done with that. He’s decided he was right in the decisions he made last week. The only person he blames for the ambush is Simon. Francis shares his frustrations about the other result of the ambush – Mary needing to rely on Portugal because France could not be there for her – with the queen and she does not immediately turn sour at the topic of Mary. She says Francis has a good heart and praises him for trying to love his future wife (she only wishes his father could do that). When Francis starts saying that his instincts are telling him not to trust Thomas and expresses concerns about what might be waiting for Mary in Portugal, then Catherine tells Francis to just let Mary go. He doesn’t listen to her.
Mary and Tomas eventually go public with their engagement, and Francis tries his best to be okay with Mary’s inevitable departure to Portugal. To make matters more complicated, Francis is clearly still into Mary, surprising her with a kiss during a secret meeting in the woods to discuss whether Tomas is really the gentleman he presents himself as.
Bash is on the road to recovery. He seems a lot better when Francis visits him to discuss the things he’s been finding out about Tomas. Once rumors start circulating that Tomas murdered his first wife, Francis makes it his business to be up in Tomas’s, creating further friction between the two men. Tomas walks in on the conversation to spout more about Mary belonging to him. Francis asserts that Mary is a friend of France and her wellbeing will always be his concern. Before he leaves, Tomas pretty much says that if they hear about Mary dying it will be because he killed her. Francis tries to attack Tomas, but Bash manages to stop him. Once Tomas is gone Bash says that if Francis doesn’t kill him, he will.
Francis has found out that getting a queen to marry him was one of the conditions of Tomas becoming his father’s legitimate heir. Bash makes the statement that if he hadn’t been ambushed then France would be helping Mary and she wouldn’t need Portugal. Everything clicks then for Francis. If Bash hadn’t been ambushed then Mary wouldn’t be engaged to Tomas and Tomas would still be unable to become king of Portugal. Francis confronts Tomas with the conclusion they drew earlier about Tomas being the spy. He’s able to get Tomas to leave Mary alone for the moment, but he doesn’t have any proof yet.
Francis and Mary quickly discuss how to go about attaining that proof. They decide that both Tomas’ servant Miguel and the prostitute who lied for him earlier will be their witnesses. Francis and Bash go to find Miguel, but end up finding out from Lola that he’s gone to the woods with Tomas. They decide immediately that Tomas is probably going to kill him. In the woods, Tomas prepares to kill Miguel. Francis and Bash get there in time to save him, but it’s not an easy victory. It’s two on one, but Bash is still weakened from his injury. The brothers pull it off and Francis ends up with Tomas at the end of his knife. Tomas threatens that there’ll be war if he dies and Francis makes reference to an execution, not falling for the threat. Tomas moves as if to attack again and Francis kills him. Francis’ hand is visibly shaking when he reaches down to help Bash up. He seems eager to put the matter behind him and get back to stop Simon’s execution, but Bash makes sure to take a moment to remind his younger brother that it’s good that killing Tomas affected him. If it hadn’t he’d be just as bad as him.
Mary, Francis and Bash arrive then with Tomas’ body and their two witnesses.
Later, after some negotiating, Mary and her friends talk about how well the talks are going. They’re interrupted by Francis coming to borrow his fiancé. 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, in the palace, Francis wants to talk politics with Mary but she doesn't want to think about the idea and wants to talk about their personal relationship. Francis, who’s apparently in a good mood today, okays that. They playfully tell each other how they feel, although in a teasing, roundabout way, and then they kiss. Later at the Harvest Festival, Francis gives Mary a boat he made for her. As their moment is interrupted, Francis is reunited with Olivia. Once Olivia is feeling better, she tells Francis what happened to her. It is also revealed she’d left court to marry another, but she the marriage fell through because her intimacy with Francis was found out. Francis tells Mary about Olivia how they were found together in the boathouse. Francis tries to reassure Mary that he only has eyes, and feelings, for her now. Of course, Mary, being the sweet girl she is, understands that Francis has to help Olivia.
Francis tells Bash about the pagan attack, and that he believes they’re luring people into the forest. Francis admits that he did talk marriage with Olivia, but it was a mistake and now he’s committed to Mary. Mary thinks it’s best that Olivia go stay at some Viscount’s estate in Paris. Olivia goes to visit Francis and brings wine. Francis tells Olivia that he’s sending her away. Olivia tells Francis that she still has feelings for him. Francis tells her that he only has feelings for Mary. Francis tells Mary that the Viscount has rescinded the offer and Olivia is no longer welcome to stay there. Mary asks him what’s really going on, and he tells her that he ‘stopped it’. She wants Olivia gone. Francis puts his foot down and says she’s staying. All the hurtful threats, she tells him he’s like his father, he threatens to take Olivia as his mistress. After Mary runs off, Francis goes to look for her and finds her kissing Bash. Mary apologizes to Francis. Sadly, Francis doesn’t seem to accept and he goes right to Olivia.
In Chosen, Francis and Olivia head over to meet King Henry’s carriage as he returns from Paris and talk about Mary’s honesty/fidelity and Olivia’s own feelings for Francis. Mary, spotting Francis waiting next to his mother, tries to talk to him about their argument, but Francis still acts cold to her. Bash brings Francis and Mary away to tell them of his concerns with the Pageans. and they make plans to keep Mary safely away from those who would harm her. Francis makes a few thinly veiled comments about secrets, trying to get the other two to come clean with him about the kiss, but neither Mary nor Bash tell him what happened.
The next day, when Mary wakes up, she’s got a freshly severed stag’s head hanging above her bed. Francis angrily tells Bash to fix this no matter what. Francis and Mary finally air out all their secrets, with Francis telling Mary that he saw her and Bash kissing. His issue seems to be more complicated than simple jealousy; Francis knew Bash had feelings for Mary but he didn’t know they were “sacrifice a human in the woods” levels of feelings, and he doesn’t like that their kiss might lead Bash into becoming into a murderer. In the morning, Bash returns to the castle to tell Francis and Mary that the debt is paid. Francis takes that opportunity to remind them that he and Mary are to be rulers, and that they can’t allow feelings like anger and jealousy to cloud their judgement. He knows that the position he and Mary are in is an awkward one (he can’t marry her unless it’s right for France, and if a better offer comes along for Mary then she needs to do what’s right for her country) so he tells Mary that in the meantime, if she needs or wants to be with other people, then he accepts that. So long as it’s not Bash, of course. Then he rushes off to be with Olivia.
In Left Behind, Francis and Charles practice dueling with forks, which, to Francis, might as well be called dinglehoppers. Mary launches into a tirade about how painful it is to watch him and Olivia prance around. Later, Catherine and Francis welcome the Italian Count Vincent. Count Vincent, Francis, Catherine, and Mary drinks some wine and engage in an incredibly awkward conversation in which the Count recounts how his son was taken hostage a few years ago and the high price he had to pay to free him. When he learns King Henry is returning, he is pleased to hear he won’t be showing up soon. Francis tells Mary to go upstairs, but a guard makes it clear she shouldn’t make a single move. The Count is clearly up to no good. He claims he’s come for payback for his son, who died shortly after his release. Then, as all good villains do, the Count reveals how he’s been plotting to takeover the castle.
Francis tries to get the Count to take a fortune of money, but the Count is being difficult. So Catherine offers up Mary as payment. Francis offers himself up for ransom instead, a far more appealing offer to the Count as he'd rather have the heir of France as a bargaining chip. Mary later clues Francis on a plan to get everyone out of the castle, but he doesn’t want to go along with it because he wants to make sure she gets out first. Mary gives a touching speech about trusting him to lead their people to safety and how he must trust her to get herself out. And then they kiss.
Francis goes takes the escape plan into motion by an killing Italian guard. Olivia, who’s been assigned the duty of standing in the creepy tunnel to open the passage door for everyone, tries to get Francis to take her with him, but he insists she stay behind to ensure Mary’s safety. She’s still not thrilled about it and reluctantly stays put.
Later as the Count almost rapes Mary and almost kills Catherine, Francis appears and he along with Mary kill the Count. He hugs Mary and takes her ladies-in-waiting to the infirmary. Later Mary confronts Francis in a fit of emotional rage and asks why he didn’t follow through with the original plan. His answer? “Because I love you.” The episode ends with them deciding to make love.
In Fated, Francis awakes with Mary in bed the next morning after having slept together. They discuss thier futures together. When a guard suddenly walks in Mary hides and the guard tells Francis that the cardinal from the Vatican is in the throne room. When he and Mary enter the throne room where Henry announces that Mary is the rightful heir to the English throne and that Francis and Mary will be wed a soon as possible. He and Mary then join Henry and Catherine to discuss the mater in private. When he and Mary are walking outside, he asks her to Marry him and trick his father into believing Mary will lay a claim to the English throne when in reality she would just be saying so to Marry Francis. When she accepts they kiss and he twists her in the air in joy.
When Mary starts to pull away from Francis, he's surprised as she was full of joy just moments before. He doesn't know that the cause of Mary pulling away from him is that Nostradamus predicted there marriage would be the cause of Francis' death. When Mary enters the throne room and says that she will not lay claim to the English throne before her and Francis have a chance to get married. In confusion, Francis pulls her aside and asks her to explain why she is planning to leave France. When he says that he doesn't believe her reasons and that he loves her she repeats what he told her in the Pilot, that "Love is irrelevant to people like us". Francis panics and still doesn't understand but he tells her to wait for him as he settles things with his father she agrees. When he comes back for her, he sees her riding away from the castle with Sebastian, his heart is crushed.
Francis has been searching for his brother and fiancée for the past week in For King and Country. Francis arrives back from his latest search and informs Catherine that the only reason he went this time was that he received word of Mary being sighted in a nearby village. As not many citizens of France have laid eyes on the Scottish queen, though, eyewitness accounts aren't the most reliable and it turns out that this sighting in particular was of a girl not more than 10 years old. Francis, seeing Catherine's hand in the disappearance of his betrothed, is bound and determined to bring her back to court. Even though he doesn't believe the reason she left had to do with his putting the interests of France ahead of her own. Mary and Bash are returned to the French Court and he presses her on the real reason that she left. He knows she believed him when he pledged to always be there for her on the morning of their wedding and Mary confesses that when Aylee died, her heart broke, though that's not good enough reasoning for Francis.
Francis goes to Mary with the knowledge that though Bash's life is at stake, she still refuses to marry. Mary finally comes clean about the prophecy and Francis has the reaction that Catherine warned of - he refuses to buy into the superstition that others have, even with the vision of Aylee's death and other weighty visions having occurred in the past. Francis thinks that Mary shouldn't let fear rule her life, yet he pressures Mary about talking Nostradamus into recanting and she begs him to stop, both for his own safety and the safety of both Nostradamus and Catherine.
Later, Catherine told Francis about Mary's decision to wed Bash. Mary finds Francis beating his brother up and stops it before too much damage can be done. She takes full responsibility for the idea and Francis lays into her for taking the inheritance from him, his mother, and his brothers, claiming that Nostradamus knows nothing and that he wouldn't forgive her.
Francis corroborates and warns his mother that if any harm fell to Bash, Henry, or Mary, the second he became king, he would execute her himself. He then turns to Mary and Bash and all but gives his blessing, telling them both that he's going to take full advantage of the freedom that he acquired for the first time in his life. Mary, Catherine, and Bash have realized that they have lost Francis and their relationship with him is completely broken.
In Sacrifice, Francis is mentioned several times and it is said that Francis has left the French Court. His whereabouts are unknown.
In Royal Blood, Francis is shown to be in Paris after leaving the French Court. He gets Lola out of situation from a debt that her brother owes. He is shown to still be heartbroken from losing Mary. He understands that Mary wanted to protect him, but Bash has his own reason of agreeing to marry Mary. He ends up sleeping with Lola.
Later, Francis hears about her mother's impending execution and Lola lies to him about not knowing anything about it. He decides to return to the castle to stop his father from murdering his mother.
Francis returns to the French Court in Consummation. Lola and Francis have stopped at a cottage to rest overnight. He worries that his mother may already be executed. He wants to get his mother exiled along with him and plans to go to Morocco. Lola says he’ll stand out there and he says perhaps Sweden. He says she may see him there and she says she hopes he settles somewhere and has a wife and family. They rehearse the cover story on why they will arrive together so Mary won’t know. The ladies help Mary get ready to go to the church when Lola shows up with Francis. He and Mary stare at each other. She asks why they didn’t announce his carriage. They tell Mary that they came on horseback. She tells her they ran into each other at a chateau and Kenna seems to know about the place and doesn’t seem to believe them. The ladies leave and Francis tells her that he’s only there to plead for his mother’s life and then he’ll be gone again for good and he’s not there for anything that belongs to his brother – the crown or the throne.
Catherine runs to Francis and hugs and kisses him. He tells her he’s going to find Henry and talk to him. She pulls him aside and tells him to forget all the warnings she gave him and Mary. She tells him that his fate has changed and that Mary still loves him. She asks him if he wants Mary, to save her life and the throne. She tells him to go to Mary and tell her that the future has changed and that they can be together. Marie comes up and introduces herself to Francis. She tells him to ride out and stop Mary from eloping and Bash getting his hands on everything he wants as he rushes off.
Francis finds Bash and tells him he knows about the elopement. He says the prophecy has been broken and they argue. Bash tells him that Mary will choose him and Francis tells him that there relationship went beyond that and Bash said there’s did too. They then begin to fight. Mary rides up and tells him to stop. Francis tells her there is no more prophecy and they can be together. Bash tells her not to listen. She asks Francis what he means and he explains. He tells her to choose him or Bash. She looks between the two of them.
Mary sees Francis in the hall and runs to him, then they kiss. She has the letter and gives it to him. It’s blank and she tells him his mother showed her what was truly in her heart. He asks if she will marry him and she says yes. They kiss again and hold each other close. Bash is drinking when Francis finds him. He tells Bash he needs to leave and never come back. He says that he had Mary but not the crown and Francis doesn't like that. He tells him to go into exile if he wants to survive. Bash argued that he needn't go if Francis was inclined to be forgiving but Francis says he’s not so inclined. Francis tells him what needs to be between them is distance if he wants to survive. In the chapel, the doors open and Mary walks in and down the aisle to Francis, her groom. Mary and Francis sign the marriage contract with their mothers looking pleased. Mary and Francis are man and wife. The crowd cheers and they dance their first dance as a pair. Mary smiles in her husband’s arms. They kiss as the other dancers twirl around them. After the wedding, Francis and Mary consummate their marriage.
In Dirty Laundry, Francis and Mary return to the French Court from their two month honeymoon in Paris. They are welcomed back by everyone and Catherine informs Francis that Bash has gone missing including the two guards that were suppose to escort him to a ship to Spain, were found dead. Bash accuses his brother of planning to have him killed and Francis tells Mary that he did not order the guards to kill Bash.
At the First Light Banquet in The Darkness, Francis comes to Mary and questions her choice of Count Nardin for Lola. Francis goes to Lola later to try to talk her out of the courtship, he says because he considers her a friend. Lola tells him she doesn’t mind if the marriage is only for convenience on his end and that she still wants to get to know him. He leaves it at that with Lola, but shares his true concern with Mary. He’s heard that the suitor ‘prefers the company of men in his bed’.
Francis also confesses to Mary what happened between him and Lola. He apologises and asks her not to blame her friend. She says she understands, and Francis is surprised at how quickly and easily she does so. He asks if Lola told her and she has to lie. Near the end of the episode, he waits for Mary to return to their room. He has First Light candles lit all around the room and when Francis tries to get intimate with her, she pulls away, telling him that they've vigorously tried to have a baby for months and that maybe tonight, they could not try. He explains that he doesn't make love to her to have a baby; he wants to have a baby with her because he loves her, a sentiment which changes her mind and the two make love accordingly.
In Monsters, as the Queen of the Bean event is being held, Francis begins to remember the past and is shown to miss Bash. When Bash returns, he is put in the dungeon and Mary wants Francis to help him but he says he’s a liar and a murderer and tells her to stay away from him because that he’s only back to try and get her back. Later, Francis decides to go see his brother only to find him with Mary. Bash explains to Francis about the sacrifices in the blood wood. He tells him there is a monster and Bash tells them about Rowan. Bash says he wants to be gone but they need to make the woods safe. Bash tells him only one has survived the monster; Olivia and she’s in the castle.
After listening to Olivia, Bash and Francis work together and take to the woods to find the threat called The Darkness. Francis tells Bash to stay close to him and Bash says he has no weapon. Francis tells him everyone despises him and that he’s made him the villain. Bash tells him he has everything and everyone kissing his ass and he has no reason to be threatened by him. Francis calls him a traitor and a usurper he trusted his brother and looked up to him only to be let down by him. While crossing the frozen lake Francis falls on some thin ice and into the water. Bash shows his loyalty to his brother and saves his life.
Bash finds Francis by the fire and asks how he’s feeling. He says lucky to be alive and tells Bash he saved his life and asks if that was wise. He asks why he risked it and Bash says he’s his brother. Francis asks if Mary knows they’re back and he says yes. Bash also tells him the guards found the cave and there was no one there but there are signs of blood and evidence of torment. Bash says the man left Rowan’s hand to tempt them onto the ice. Francis promises him he will track and kill the man and tells Bash he can leave assured of that. He tells Bash he deserves his own life far away from there. Bash says maybe he can find something of his own and Francis says he will and will still be his brother. They learn that it was Henry who ordered the guards to kill Bash. Henry says Bash is a threat to everyone and draws his sword. Francis defends Bash and Henry says when people don’t listen to the king they must be dealt with. Francis tells him that he saved his life and pursued his enemies. Francis says if he harms Bash, he harms himself. Henry puts down the sword and says he is pleased to see them getting along again. He says he knows just the thing to preserve this harmony and says if it doesn't work, his sword will take two lives.
In Liege Lord, Mary and Francis receive more wedding gifts. She gets a bridle and Henry jokes that Francis should try it on his wife to keep her in hand. Everyone laughs and the couple goes off to dance. They worry about Henry’s increasingly erratic behavior and she says France can’t be run by a mad king. The good news is that he’s obsessed by Penelope so he’s distracted while Catherine is secretly running the country. Later, Mary speaks to Francis and tells him that if she dies without an heir, Scotland will go to France. He’s not happy and says it’s typical of his family’s trickery. The contract was pages long and in Latin. Mary says his parents did it to keep the upper hand. Francis says that once they get Scotland from her death they can invade England. She begs Francis not to tell his mother yet and says she can get access.
Thanks to Kenna, they receive the contract without her signature and Francis says it’s a contract for them to kill her. Mary says she will write to her mother but Francis reminds her that her mother helped write it and says that the treasury gave her mother a large payment on the day the contracts were issued. She wants to force their parents to change it. Mary thinks they can give this info to the Protestants in Scotland and that would force their parents to destroy the other copies of the contracts so there is no evidence of their hijinks. Francis says this will give her mother a hard time and Mary says as Queen of Scotland, it’s her duty. They plot on how to get a letter out because Catherine will stop any letters going to Protestants. Mary suggests they host a party. Catherine is uncomfortable and unhappy about the Party For Scots. Francis and Mary discuss which will take the news public rather than going to her mother, Marie, with the plot. They discuss one man in particular that used to serve Mary’s father.
Francis invites Lord McKenzie to speak with Mary. As the go into a room to speak in private, Mary informs Lord McKenzie and his men of how the secret contract her mother signed. She says she has the heart of a Scot and says that France has betrayed them. She charges them to take the news and tell the world - especially Lord Hardy – the Protestant leader. He and his men lay their swords at her feet and bow and he calls her your majesty and kisses her hand. He says they have waited a long tie for her to rise. Francis tells her it was amazing and says she’s a liege lord to those men. She says no one has ever looked at her like that. Mary says she’s been used as a chess piece for too long and he tells her she should claim and keep her power.
The next day, word of Lord McKenzie and his men's deaths gets out. After Mary confronts Catherine, Francis hugs her as she cries. Francis tells his mother he’s surprised that she’s releasing the bodies to Scotland. Mary comes in and demands the contract. Catherine tells her she’s won and Mary tells her that she can hand it over or she will spread the word that Henry is mad. 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. At night, 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 pats his cheek. He’s a bit shocked. They lie down in bed and she blows out the candle.
In No Exit, during Lola and Lord Julien's Wedding, Francis and Mary meet Cardinal Morrisini, the new Papal Envoy. He planned on meeting with Henry concerning rents and tenancies, money that the French desperately need, but since Henry is off in his own world recently, Mary takes things into her own hands. She walks over to the Cardinal and instantly charms him, getting him to agree to meet with her and Francis over the rents and dance with her so the two could discuss their terms. The next day, Francis learns that Mary wants to return to Scotland with her half-brother, James Stuart. Francis isn't so sure about it, suggesting that they send diplomats in her place. He believes that France is truly unstable right now and that if things don't go well with the Cardinal, Rome will withdraw their support, thus leaving his country to look weak before the world. This would invite challengers to come and overtake France and as we all know, Henry is in no position to lead a military mission, so Francis argues that they need to lock down Cardinal Morrisini's support before even thinking about leaving for Scotland. However, Mary notes just how much of her life at court has been geared toward bending for France and addressing French problems, so she still wants to go to her country, Francis support or no Francis support.
Bash gives Francis advice on putting Mary first and how it's okay to be a bad king sometimes. Francis goes to Mary and assures her that he's willing to go to Scotland with her, as long as she'll wait until things with the Cardinal are squared away. She agrees and the two begin planning for France. At night, Francis and Bash see James' footman paying one of the higher-end castle prostitutes and bring him down to the dungeon where they question him about how he could afford this, why he was using English coin to pay, and where he was headed after he paid the prostitute. When the footman won't talk, Francis calls in the torturer. However, Mary trusts her brother. Francis suggests that maybe they were going to kill her on the way to Scotland and he gets time from Mary to produce proof that this is all a set up against her.
Francis tortures the footman in the dungeon and bribing him to give up information regarding who he's working for. Once Francis mentions that he'll pay ten times what the man got from his first conspirator and allow him to leave scot-free assuming his information pans out, the footman mentions that he was paid by a group of people who wanted to assassinate Mary before she arrived in Scotland. Francis informs Mary of James' motives and she refuses to believe him. Mary tells Francis that she's going to Scotland, he has her thrown in the tower. He says that she'll be there until James leaves and he can assure her safety, but she calls him a liar and accuses him of doing this for his sake rather than the sake of her and her country. If Scotland were to fall while she is locked away, she'll never forgive him.
A month goes by the events of No Exit. Francis' relationship with Mary is deeply strained as he locked her up in the tower and she barely speaks to him. Francis tells Mary that they need to send armies to help her mother. She says his father won’t help and he says they will go together to appeal to his mother. They get the news of Elizabeth will become the next queen of England. Henry comes in and says that Mary Tudor is dying but managed to pay the gold to give her crown to a bastard Protestant. Henry rants at Mary and asks if she’s pregnant. He calls her useless angering Francis.
Later, Francis goes into Mary’s chamber and finds her angry that none of her Catholic allies will come to her mother’s aid. Francis says he tried to find help as well but they all ask what the king thinks and they can’t refer to him since he’s gone nuts. Mary is writing to her uncles for help. She’s writing to the Duke of Guise and Francis cautions her and says he’s dangerously ambitious and has built an army from stolen boys. She says she doesn't trust him but that’s not a luxury she can afford. Francis along with Mary meet the Duke of Guise. Mary admits they need her help with Marie and asks what he wants in repayment. He says he wants a permanent position at court – Lord Magistrate of France – a position that would make him the king’s right hand. Francis reminds him he was sent from court for being too grasping. Christian says he served the king, not challenging him and he ran the country while Henry was out making bastards. Francis tells him that he could simply take his army and Christian tells him that they won’t follow a boy waving a crown. Mary tells her uncle they will let him know and he walks away. She tells Francis she knows Henry will never agree and he says he has to or she’ll lose Scotland. Francis invites Mary’s uncle into the throne room, telling him he thought about the request. Francis knows that Henry will never appoint him, but that was not the real plan all along. Francis will be the next King of France, so the future of the country is in his hands. He will agree to appoint the Duke of Guise to the position that he wants, when he is King, as long as Francis will be the one commanding the army. The Duke of Guise agrees, since he doesn't think it will take long for Francis to take the throne. Mary was not invited, since they both know she will not allow Francis to agree.
Francis tells Mary that her uncle will send enough people to Scotland to save her mother and her throne. Francis says he will be going to Scotland as well, in order to ensure her mother’s safety. Mary knows Francis is saving her country, but is still worried for Francis’ life then passionately kisses him. While in bed, he hopes that Mary isn't the only one waiting for him when he returns.
Henry knows that Catherine and Francis have been working behind his back and cancelling his plans. So he had already sent out troops in order to go to war with England. Catherine tried to talk some sense into him but he refused to listen. Looking over the plans, Francis realizes they will be able to win but only if they have a second army on the other side of a frozen marsh. Catherine knows he is talking about the Duke of Guise's army, the one who is supposed to go to save Mary’s country. Francis knows Mary will be angry but they will lose their entire army if he doesn't do it, which would make both France and Scotland vulnerable to England.
Mary is angry that Francis is taking the army meant to save her mother and her country, in order to save France. He claims he cannot defend Scotland without ensuring France’s safety, but Mary says he has never defended Scotland with anything other than words. Mary calls their marriage a mistake, saying she should have done many things but didn't because she loves him. He claims he will go to Scotland as soon as his war is over, but Mary does not believe that will happen. She wants him to promise her two things, that he will no longer make promises he cannot keep and that he will return to her alive. Francis is last seen leaving with his army.
Francis goes into battle in Higher Ground. Francis leads his men against the English forces, they arrive at a French outpost that recently pushed back the advances of the English army. With their commander dead and their ranks cut in half, they want to retreat back into the outpost and hide from the upcoming fleet of English soldiers, but Francis knows that they can't keep doing the same thing and expect to defeat the English. Rather than allowing themselves to be picked off, Francis convinces the 12 men that they should move toward and seize a castle with the help of the Duke's men. To solidify his stance, he gives up the protected position of noble and becomes their new commander in the field.
Francis and his men get ambushed by English forces a few miles from the English line. With an assist from Leith, Francis is able to fight off the assailants that come after him and he doesn't lose many men along the way; however, because he put the noble colors on another of his forces, an innocent man lost his life, as England targets the nobles in battle before anyone else. Francis comes up with the idea of shooting a flaming arrow into the English's ammunition, causing a massive explosion that would take each of the enemy soldiers out. He wants the men he's with to charge one way while he goes another and sets up the shot, but Leith tells him that they're too used to generals and Lords treating them as chess pieces and that they're not going to agree to the plan because of his status at court. Francis wins the loyalty of his men by promising he doesn't see them as chess pieces, and proves it by making sure they make it out of their mission alive.
Following his tatic, the men draw the attention of the English cannon atop a cliff while Francis fires a flaming arrow into their gunpowder, sending the entire encampment up in a huge explosion, winning the day. Although not without cost, as Leith is critically wounded from one of the cannon shots. Leith pleads to be left for dead, but Francis begs him to think of someone he’d like to see again, a person worth fighting for. Without naming names, he tells the story of his romance with Greer. and how it could never work due to their class differences. It’s then that Francis tells him that Kings can grant land and titles, and since Leith has just made a friend with the Dauphin of France, that’s exactly what he’ll get. This final push of encouragement, as Francis tells him to live on for Greer and for himself, inspires Leith back up to his feet. And right on time, too, as French forces regroup to march on Calais.
Francis returns to the French Court in Long Live The King after being gone for months and is reunited with his wife. Francis announces that they have taken back Calais from the English. King Henry welcomes back his son, with the announcement of Queen of England's death. He wants to declare war on England, as he wants to put Mary on the throne of England.
After Francis and Mary have a passionate reunion, Mary tells Francis that she does not want to stake claim to the throne of England. She fears that there will be war if she does that. Also, Mary does not want her cousin, the protestant who is set to be England's Queen, to see her as an enemy for life. Francis assures Mary that he will support whatever decision she makes, and stand by her. He tells her that she can count on him, like the way he counts on her. Mary tells Francis that she plans to write to the Queen in waiting.
Francis with his wife and his mother find out that Henry has started planning his attack on England and they realize that if a war happens, thousands of French men will be slaughtered. Catherine wants to stop King Henry, implying that the King should be killed. Francis objects to that. He wants a chance to convince his father that a war will not be in the best interest of France. Francis takes his father to hunting to have a one to one talk with him, trying to break through to him one last time. After father-son bonding, Francis manages to convince his father and comes back to know that Catherine has made arrangements to kill King Henry. He is furious and lashes out at Mary, as well.
In the season finale, Henry summons everyone into the courtyard in the middle of the night and informs them that he knows one of them, one of his friends and/or family members, wanted to have him killed. Therefore, he's hired new men loyal only to him and swears that when the sunrises, his sword will cast a shadow on the guilty party. He then turns to the secretary to Lord Bellamy and asks if the man went to confession; though he did, he never took the Lord's name in vain or fornicated, so Henry kills him due to how prepared he is to die. Francis realizes that his father is beyond help. He meets with Mary and Catherine to discuss their options. Francis’s plan is to find the generals that Henry had previously dismissed, and seize the throne for himself.
Francis goes on his way to find the generals he needs for the coup. Instead, he runs into the dead bodies of the men that died in the ship explosion. The soldiers overseeing the corpse removal tell Francis that there is going to be another ship-joust tomorrow, and that there are also 3000 men leaving soon to march on England. Francis decides to take matters into his own hands. He fatally wounds his father in a joust, but the thing is, no one knows it was Francis who was his opponent.
Henry isn’t expected to live the night. While speaking to his father whom is on his deathbed, Francis learns that he was named after Henry’s older brother, the man who has been haunting Henry. Francis has many of the same qualities of his namesake, including what Henry percieved as the inability to leave. Henry killed his brother long ago, on a tennis court, after he poisoned his water. Francis thinks this is why Henry tried to turn him from his own brother Bash. Henry warns Francis that his deeds have haunted him his entire life. He looks to the end of his bed, sees his dead brother and asks if he can let it go now. Henry dies and Francis asks for forgiveness. Francis leaves Henry’s chambers and the first person he sees is his brother, Bash. As Bash attempts to kneel before his new king, Francis won’t have it and pulls his brother into a hug.
The next day, Francis joins Mary, saying he was up all night talking to nobles and advisers, since he is now the king of France. He wants to tell her about what he has done, but Mary convinces him it was truly an act of God. She begins to tell him of the choices she has made, of the woman it is turning her into, and she is afraid he won’t love her. He wants them to share their burdens, to have no secrets between them, and at that point they might be able to forgive themselves. Before they can continue, Mary receives a letter from Lola, which she reads. Mary tells Francis he should go to Lola, since he is the father of her child. Lola finally wants him to know as well. She begs him to leave and to go to her side.
Outside, Mary tells Francis about the Plague, but he decides to leave. She warns him of the dangers, that he is now king and he cannot continue to think with his heart. He tells her that he will not leave what might be his only child alone to die, and that he wants to be a compassionate king. When he leaves the castle, Mary orders the gates to be closed. One of the guards mentions Francis, but she tells him that the king knows of the risks. Once the gate is down, Francis looks back at Mary before continuing his way.