I was wrong. What I asked of you, the backward step. You must know. I want the same world as you do, the better one, and the only way to field it is together. We do greater things when we act as one, when we trust each other as equals. This is not a coronation for a King. It is for a King and Queen.
In the season premiere, Mary is worried about Francis as he went to go to look for Lola. She is shown to be heartbroken as she did not want him to go. After Francis finds Lola and the baby, he wants to hurry back to Mary. Catherine supports Mary by telling her not to let Lola come between her and Francis.
Mary and Francis are reunited in Drawn and Quartered. As Francis arrives, he quickly hugs Mary but with Mary seeing Lola and the baby, causes tension for her and Francis. Then Francis introduces her to his cousin, Louis Condé who helped Francis and Lola. Mary thanks him and Francis takes Mary inside and the two have their first sexual encounter since he left to be with Lola. However, afterwards, she admits to feeling pressure from Lola's presence at court, seeing as how it only magnifies the fact that she's yet to get pregnant, and urges Francis not to claim Lola's child in order to give them more time to conceive. As the royals gather to celebrate Francis' homecoming, Narcisse and his band of men interrupt the party asking for justice for Éduard Narcisse, as Nostradamus had earlier assured Narcisse that his son had been infected when he was taken to the catacombs. After talking to the survivor, though, he knows that to be false and that Eduard was deliberately infected, so he wants the murderer to be punished without impunity. Meeting in their chambers, Francis and Catherine gang up against Mary, with the former upset at his wife making a rash decision and the latter mentioning that the nobles could lead an uprising if they're not happy with the royals. While Mary vows to fix her mistake and spare the lives of the guards who brought Eduard to the catacombs under her command, as well as Nostradamus.
Later, Mary meets with Francis, who chides her on being reckless with Eduard. However, she hasn't taken kindly to Francis abandoning her in this situation, nor has she forgotten the fact that he abandoned the kingdom and left her to fend for himself. While she's got the opportunity, Mary gets in a shot about Francis choosing Lola, of all people, to have sex with, but since the two don't have the time to fight right now, they decide on looking for blackmail evidence that will get Narcisse to back down.
Just as Nostradamus execution is held, Mary interrupts the execution claiming to have a hand-written confession from Lord Voland, a confession that had been sent to Rome earlier. Francis comes around, though, with two letters in his hand and succeeds in shoving her out of the scene; he uses his title to get some time alone with Narcisse and makes a bargain that Nostradamus and the two guards live if Narcisse can get some additional land. It turns out, though, that the entire thing was staged, as Mary didn't have anything in the way of legitimate written confessions. At the end of the episode, Francis meets Mary in the nursery, she then tells him that he should give the baby his name, making it safer than it would have been otherwise.
Mary and Francis are crowned Queen and King of France in Coronation. Francis tells Mary that they are better together as equals and this coronation is for a king and queen. They enter the room and Francis kneels. The cardinal slips a ring on his finger and offers him the scepter and then sets the crown on Francis’ head. Mary smiles. Francis stands and takes his throne. They all recite – long live the king. Mary kneels and receives her crown then takes her seat at his side. They say – long live the queen. Petals rain down on them as all applaud. In the final scene of the episode, Mary and Francis are making passionate love.
After reminiscing of their childhood, Mary announces her pregnancy to Francis in The Lamb and the Slaughter. Both overjoyed, the two go into their chambers to make love in celebration. They are then interrupted by Catherine who barges in and is exicted that she is going to be a grandmother. Mary questions her on how she knows and Catherine reveals that she used her spies to confirm her suspicions that Mary was with child. Since this gives Mary a better shot at claiming the English throne from childless Elizabeth, Catherine is willing to do everything she can to help Mary, including bringing food and tonics to help with the baby's growth. During a party that night, Francis becomes more attached to Mary during her pregnancy. The next day, Francis found out Mary was to become Jean's godmother which he greatly approved approved.
After the christening, Francis quickly went to Mary who broke the news of her misscarriage and they both mourn over the loss of their baby. During the night, Francis took Mary out of the room and to reminisce about their childhood when they used to chase fireflies. When there were no fireflies, Mary would cry but that was not why Francis was happy. It was because he waited for those fireflies with Mary. Japanese lanterns were floating in the sky to give Mary the fireflies that she deserves. He then told Mary, “Whatever the future brings, you are my light.”
In Blood for Blood, Mary and Francis deal with a Catholic attack on a Protestant church and Condé's nephew being murdered by them. When Francis and Mary decide the Catholic offenders should be hanged and the Protestants will be punished after they started revolting in the villages. However, Narcisse interferes as he got Francis' confession of killing King Henry and he uses this knowledge to threaten and take advantage of Francis’ weak spot. Narcisse tells Francis that if anyone finds out, he will have Mary and Francis killed. So Francis has to go against all his and Mary's plans and let Narcisse's men go. When Francis tries to hide his sins from Mary and protect her from Narcisee, she grows more and more frustrated and annoyed with him. She pushes him for answers, thinking that he’s avoiding her because she lost the baby. He let’s her believe he’s angry, upset, and disappointed over their loss. This greatly hurts her.
Due to being hurt by Francis' words, she informs Francis she will be traveling with Catherine to Beauvais in Three Queens. Mary and Catherine are attacked while out on the road and as Francis hears of his wife and mother are missing, he sends out a search party and also heads out himself. Near the end of the episode, Francis finds Mary and they embrace. After, returning to the castle, Francis helps Mary off of her horse and tries to talk to her but she tells him that she is tired and retires to their chambers. Catherine tells Francis about how Mary nearly got killed trying to see a physician and please Francis. She tells him to trust his wife and be honest, because if he doesn't, she could end up 1,000 miles away playing her rule out of duty. While in their chambers, Francis quickly tells Mary that he didn't mean what he said about her uterus. However, he’s still not ready to tell her the truth about Narcisse. He promises to fix the space that’s between them, but based on Mary’s face, it might be too late.
Going into the next episode, Mary and Francis are still at odds and to push them even further. Narcisse still continues to blackmail Francis and presents a new law. He wants every person in France to have to declare his/her faith publicly in front of the King which will bring riots and threaten the lives of Protestants living in a predominantly Catholic country. If Protestants lie and say they’re Catholic, there’s the risk of being killed for lying to the King and if they tell the truth, they will still be killed anyway. Mary gets Conde to help her rally up some Protestant nobles who would be willing to publicly identify themselves as protestants and urge Francis not to sign the bill. The plan works and thanks to Mary, it brings them closer together until Narcisse threatens to have Francis' entire family killed. Francis decides to sign the edict in order to protect his family. Mary confronts him and she is furious. Still unable to tell her the truth, she tells him he’s not the man she fell in love with anymore, nor the husband or King he once was. She’s been waiting for him to come back but now she’s done. Francis then tells her to leave him and go back to Scotland. She silently cries and walks away as Francis sits on his throne.
In Terror of the Faithful, Mary blames Francis for his actions and tells him that while she may have decided to give up on him but she's not giving up on France. Bash tells Francis that if he keeps pushing her away, he will lose her. Francis only wants for her to leave so she'll be safe from Narcisse. Conde brings the minister to request the sovereigns’ permission to rebuild the Protestant church. He orders Francis to expel the ignoble Cardinal Vasari and threatens that if these needs are not met, he has explosives set to blow up Catholics. Francis has him arrested, and swears he will find these explosives, even if he has to bleed the minister to find the whereabouts. Bash and Condé set off to discover where these explosives are. Francis pretends not to care for Mary's opinions and leaves. Later, Lola tries to get Francis to tell Mary the truth about Narcisse but he refuses as he is trying to protect everyone from death. After questioning the minister, Mary, Francis and the others find no explosives in the location that the minister told them of. Francis takes things too far and minister’s bone is dislodged from the socket, causing his death. They soon find out that their were no explosives. By the end of the episode, the peasants and townspeople believe it was the crown that killed the minister. The renegade Protestants have made a martyr of the minister and the people stand up in revolt against the Cardinal’s soldier and the crown. Mary tells Francis that this is his fault. She has lost all faith in him and the man she thought he was.
In Acts of War, Mary suggests to arrange a marriage between Conde and Claude as Conde would help bring known Protestant blood into the royal family. Francis agrees to Mary’s idea but only after he is threatened by Narcisse who is continuing to blackmail him. During a party, Mary tells Conde that marriage is about love and faithfulness and wanting to only be with one person in the world. She believes in Francis because she loves him. By the end of the episode, Mary is raped by Gerard, the father of the minister as revenge for his death. When Francis returns and is ready to tell Mary the truth about everything, he is informed of her rape and vows to kill her rapist and attackers.
As Mary and Francis continue to search for her rapist and attackers, he finally tells her the truth about him killing his father and Narcisse's blackmail. Francis tries to explain to Mary that he was trying to protect her . Mary also moves back to her old chambers as she can't be with Francis right now nor can she stay in the room where she was attacked as she is still struggling from the event. Francis confronts Narcisse about the attack on Mary and makes him his prisoner. The next day, Mary tells Francis that the men who came after her are dead but she blames him for her rape. She wants to be his wife only in name and live a life separate from him. Francis refuses to live like that and he loves her. For Mary their love has caused her too much pain.
After trying to reconnect with his wife, Mary decides to get away from the French Court and visit their chateau, needing time away from him. After getting advice from Greer and being able to help Conde, Mary returns to the French Court as she doesn't want to be distant from Francis anymore. When Mary goes looking for Francis, she finds him asleep on a nursery bed, with his son and Lola. She looks deeply hurt and leaves without waking him.
In Banished, Francis continues his attempts to get close to Mary again after she caught him sleeping on the same bed as Lola and his baby. She continues to distant herself from as she is hurt by the action knowing that they could have that life together. Francis tries to prove to her that the happy life he wants is with her. He gives her the space she asks for and he also distant himself from Lola. They continue to work together as rulers, that is until Francis sees Mary touch Conde’s arm, realizing her fear of men has changed. At the Ice Festival, Conde gets snappy with Francis, causing a fight between the two which Francis wins. As Conde tries to go at Francis again, Mary stops him from attacking her husband. Mary rushes to tend to Francis after he receives a cut on the face from Conde. Francis decides to call her out and by telling her everyone now knows Condé has feelings for her. And if they decide to lead separate lives, it would be a threat to their marriage and their rule. Francis then tells Mary he knows one day she will have his son and that the paternity cannot be questioned. Mary gets defensive over his claim but Francis is quick to assure her he understands just how fair it is. Mary decides to ask Lola to be with Conde in order to keep him away from her. During the night, Francis visits Mary in her chambers and asks if he can stay with her, only to watch over her and will sleep on the couch. She happily allows it.
In Sins of the Past, Francis plans to move Mary and himself away from the castle and the painful memories but it is put on hold due to King Antoine arriving at the French Court and asking for money. They are against it as he has been seeking aid from Queen Elizabeth. But not wanting to start a war, Francis and Mary agree to financially support Antoine’s country. During the night, after Francis has been spending countless nights on the couch in her room, she invites him to sleep in the bed with her but to only sleep. Later, Mary jumps out of bed due to not being able to take the sound of Francis’ breathing which brought back memories of her rape. Francis comforts her and tells her: “I can tell you that what happened was a nightmare, and the nightmare is over.” He opens his arms for her and she walks to him, letting him hold her as she cries. The next day during the night, the couple are happy while dancing together at the Winter's Ease Feast. However, after learning that they are threatened by England again, Mary decides her and Francis should lead separate lives. He is against it but she tells him she wants him to find love with another person because she loves him and at least one of them should be happy.
In The End of Mourning, Francis and Mary learn that Catherine and Narcisse had discovered their family bible had been poisoned and it’s what led to Henry going mad and made Catherine ill. Mary, Francis and Bash plan a dinner for Condé to get him to postpone his trip with Lola and calling off their continued relationship. Francis and Mary eventually gather Conde and Antoine around the table to lay out their accusations. Just as Francis is laying out his suspicions, Catherine tells Francis that Narcisse has discovered evidence that it was the Duke of Guise who was behind what happened to Henry. Conde is furious at the accusations levied against him and lashes out saying that Bash killed his brother. However, Bash is not at fault as he was under orders from Henry to kill him. Mary continues to push Francis away with her growing coldness and causing him to close off his heart.
Mary and Francis plan to conceive an heir in Forbidden. Mary learns that her power in Scotland is being threatened. Elizabeth is still trying to take over Scotland and conquer more of Europe, including France. In order to help secure her power, Mary needs to have a son. Mary tells Francis about her political problems and tells him she wants to try to have a child soon. They agree and also make sure there are witnesses to see Francis going to Mary due to their separate chambers. They only get as far as kissing on the bed before they stop. Mary’s emotional wounds are still too raw and Francis just isn’t comfortable being forced to be intimate with her rather than wanting to do it out of love. However they begin to fight as Mary confesses that she has feelings for Conde. Francis refuses to be with another woman as he wants to be with Mary, so he forbids her from getting any closer to Conde.
In Tasting Revenge, Francis allows Mary to be with Conde. Lola convinced him that Mary needs time to heal away from her pain, and that Conde is the way for her to do that. Francis loves Mary so much that he’s willing to give her that freedom.
In Tempting Fate, Catherine informs Francis of Mary's betrayal of her planning to return to Scotland with Conde and leaving Francis. As Francis hears of this, he collapses and becomes ill.
Mary learns of Francis' collapse in Reversal of Fortune. Mary returns to the castle and Catherine lashes out at her. She knows of Mary’s plan to run away to Scotland with Conde. She blames Mary for Francis’s illness, saying it’s a wife’s job to know the well-being of her husband but instead, Mary was with another man. She also never imagined that Mary would kill Francis by breaking his heart. Mary goes over to Francis' bedside and begins to cry, sorry for everything that has happened. Mary eventually gets word that a Protestant army was preparing to attack Scotland. Mary chooses to send France's troops to Scotland in order to save her country, which angers Catherine even more and would once again be betraying Francis.
During the night, Mary returns to see Francis and cries. She tells him that even though the past months have been hard and she hasn’t been able to be near him, she can’t imagine never hearing his voice again or being able to touch him. As she holds his hand and continues to cry, Francis suddenly wakes up. The next day, Francis informs Mary and Catherine that he has chosen to send two thousand men to Scotland to fight the Protestants. After Catherine leaves, Mary questions him on to why he is doing this. Francis asks does she mean why when she was planning on abandoning him and France. He says his country made hers a promise and they are allies and stronger when they honor their promises. He will use his second chance in life more wisely so he has no regrets which makes her ask him if he regrets marrying her. He tells her that she should leave. She asks if he means this room or France. He says it’s her choice but to never expect a welcome from him or his trust ever again. In the end, Mary tells Conde that she’s decided to stay in France and remain with Francis. She returns to Francis' chambers and watches him sleep.
In Abandoned, when news of raiders have killing a priests and holding children of the church hostage, Francis comforts Mary with words but pushes away from her learning that she is still together with Conde. Bash comes to Francis, telling him that three of the men killed that were part of the raid, wore Conde’s seal. When Mary hears of this, she pleads with Francis that Conde could never have done this. After this, she realizes she can’t continue to see Conde and breaks it off with him. Francis informs Mary of Conde’s proxy marriage and finds out that she knew Elizabeth courting Conde and but he swore he would reject her proposal. Francis becomes angry with her and tells her that she may have caused the end of their reign.
As Francis is trying to capture Conde in Fugitive, he finds out that Mary tried to help to Conde escape the French Court. Francis decides that he cannot let Conde live as an English King-Consort on French soil is too dangerous to his reign. If Conde becomes King, it will cost Francis his life. Mary tries to receive forgiveness from Francis but he refuses as long as there’s a threat to the throne on the loose.
Francis and Mary find out that Conde is planning to lead an English army to overthrow the crown in The Siege. Francis' siblings are too young to rule, nobody would support Catherine as Regent and Conde has a direct line to the throne. Mary tries to apologize to Francis about everything that has happened but her words have no meaning anymore. Later, Francis decides to evacuate the royal family including Lola. Mary offers to stay but Francis wants her to be safe as he was unable to protect before, not wanting to fail again. When Mary leaves the castle, she is captured by General Renaude and his men. After she realizes that she’s been tricked and Renaude has switched allegiances, her guards fight Renaude’s men long enough for her to escape and warn Francis. Back at the castle, she tells Francis and Bash of Conde’s army and Renaude’s betrayal. Francis, Mary, Bash and Kenna hear a commotion outside and see Renaude and his men arriving, starting an attack. After Renaude's has been defeated, Kenna tells them that Conde has French Protestant lords and their men on his side and says Renaude told her.
Days later, Conde’s army arrive at the French Court. Francis agrees to a meeting with Conde and rides out to the enemy lines. Conde asks for Francis to surrender and give him the castle, the crown and Mary. Unable to trust Conde with Mary's life, Francis refuses. Francis knows that Mary wouldn’t be safe from Elizabeth’s clutches even if she promises to leave her alone when Mary marries Conde. Francis returns to the castle and explains to Mary what had happened. He says he thinks he can save her but Francis says Conde won’t be able to save her from Elizabeth and says tomorrow, without a miracle, they’ll both be dead. Mary tells him that it’s not the end she dreamed for them. Mary then shortly comes up with a plan that will save Francis' life so she heads to Conde's camp.
Francis and Mary reunite in the finale. Mary's plan against Conde worked and Francis finds her beside a wounded Conde. She tells Francis that she planned the whole thing and did so because either him or Conde was going to die and she couldn’t let it be Francis. In the end, she chooses Francis because she loves him, she always has and always will. They return to the castle and celebrate their victory. Francis has decided to save Louis as a bargaining chip to assure an alliance with Navarre. Catherine disagrees, and she orchestrates an elaborate plan to kidnap Lola and lead Francis to believe Conde’s men killed his son. This way, Francis will show no mercy and kill Conde immediately. When Francis finds out of his son's death, Mary comforts him. Narcisse finds out of Catherine's betrayal and informs Mary of this. After Mary tells Francis of what Catherine has done, he banishes his mother from the French Court and rips her of her titles and money.
Later, Mary and Francis meet in her chambers. He tells her he didn’t think he’d be able to forgive her, even if it took years. Mary claims she’d wait, because she loves him. He believes she’s proven that. She wants to know if they could recommit to each other, love each other again. They then begin to kiss and end up in bed. After making love, she tells him she’ll love him for the rest of her life, and never let him go again. Later, Francis meets with Nostradamus and hoping Mary will be pregnant with his child. But unknown to Mary, Francis is dying.