Many weeks after Condé's escape and Catherine's betrayal, Mary's relationship with Francis has grown stronger than ever and things are going well between them. Mary is first seen learning dances from her ladies, soon having a passionate love session with Francis and eventually discovering him working on a boat. Enjoying their happy married life, they eventually go to back to their lives as rulers. While trying to deal with the continued crisis in Scotland, they are informed by Narcisse that their Catholic allies have turned against them leaving them with no resources. Looking at Francis' boat, Mary comes up with a plan. In the throne room, Mary and the others meet with Martin who comes with a tiger as a gift. In exchange for his help, he is looking for a wife and has his eyes set on Greer. After talking to Greer, Mary hesitatingly agrees to Martin's offer.
Later, Mary and Francis receive a letter from her cousin, Elizabeth, asking for permission to marry Prince Charles, which implies a truce in Scotland. Mary wants to agree to the offer since she feels she would be the one in more power. Francis can't agree to it and confesses that he is dying. Charles will take the throne and cannot allow him to marry Elizabeth. Shocked to hear her husband will soon die, Mary breaks down in tears as Francis holds her. In the chapel, as Francis comforts Mary, he promises that he will make political preparations so as not to leave Mary unprotected when he dies. Mary and Francis are soon informed that Catherine killed herself after her Monk lover died from a lumber mill sex injury. They know it's a decoy and discover Catherine is in England. The next day, they capture Catherine with Martin's help and has her tossed in a cage with the tiger. Mary isn't sure which one needs thicker bars, Catherine or the tiger but believes he will sure more.
Following Catherine's capture, Mary begins to make tough choices in order to secure her and Scotland's future in Betrothed. Francis thinks that after his death that Mary should marry Charles and she isn't thrilled about the idea. Being able to marry the first time for true love, Mary sucks it up to having to marry for political reasons this time. Now that Francis and Mary have agreed on everything and know what their plans are, they gather the rest of the family to fill them in on Francis’ fate. Charles isn't ready to become a king and he isn't happy about the idea of marrying Mary and it is explained to him that him marrying a queen, they’ll circumvent the need for a regent to rule until Charles comes of age. Later, due to Charles' recklessness, Mary and Francis reveal that they have been spying on Catherine and stop the assassination plot on the Bourbon family. Catherine defends her actions; the Bourbons are a real succession threat. She reminds Charles and Mary who was behind the latest attempt at a coup.
Eventually, Charles agrees to marry Mary. Francis tells Mary that Charles will need her and she cries about a future without him. He then holds her in his arms. By the end of the episode, Mary goes to see Catherine once again. She informs her that she will be marrying Charles and since Francis refuses to have Catherine put to death, Mary may have better luck convincing Charles. Catherine demands an audience with Francis, and that request is denied. After Mary leaves, Catherine begins slamming her head against the door in an attempt to injure herself.
Mary's relationship with Francis becomes even stronger in Extreme Measures, as his condition starts to become worse. As Mary tries to talk to Charles about their countries' alliance, he soon becomes distracted by the Duke of Toulouse’s daughter, Constance, and Mary ends up having to deal with the new English ambassador, Nicholas, who wants to see Francis. Mary is left to tell him that Francis is away at Reims but will be back soon. She later goes to see Catherine who is demanding to see Francis. Mary tells her that Francis never wants to see her again and keeps her locked in her cell. Mary barely has time to fill Francis in on Catherine’s antics when Bash comes into their room, saying that Antoine has returned. Mary goes to see him and he requests that Condé be granted safe passage through France. To get this from the crown, he’s willing to convert to Catholicism and credit it to Mary. She is willing to agree only if he renounces his claim to the French throne. He refuses, claiming that she is the woman who destroyed his brother. When Mary brings Francis to talk to Antoine, he collapses before he even gets there.
During a party for Antoine's welcome, Mary shares one final dance with Francis. Later, Mary is informed by Bash that Antoine has been negotiating with Nicholas on not giving up his claim to the French throne. Mary uses her last resort which turns out to be Catherine. After Catherine gets Nicholas to back down, Mary and Francis confront Antoine. Once Francis' illness starts to show, Antoine begins to refuse to sign away his claim knowing that Francis is dying. Francis shows him that a dying king is his worst enemy; by killing Antoine's bodyguard and threatening the entire country of Navarre. Antoine gives up his claim to the throne. After telling Francis that France will no longer be able to protect her and she can't marry Charles, they attend Lola and Narcisse's wedding and release Catherine from prison.
In The Price, Mary receives a letter from her mother that there are English troops in Scotland and as Francis refuses to look weak in front of his enemies, he decides to send France's best warships to Scotland. However, the two ships were sunk and hundreds of French lives were lost. Mary then tries to make a trade with Nicholas; two captured English generals for the removal of the English troops. Nicholas refuses and then goes to steal the cipher that Mary and Marie use to communicate. While Nicholas is at Greer's brothel, Greer gets the letter Mary sent to her mother. Nicholas fell for Mary's plan and the ambassador has bad intel on Elizabeth. Eventually, Francis illness takes a turn for the worse and wants to spend his final moments with Mary. As they talk about their family and future, Mary begs Francis to keep fighting but he is no longer able to and dies. Soon Charles, Bash rush in with and have brought Delphine with them. Mary and Charles are warned by Bash that if Francis is brought back it will come with a price. Mary begs Delphine to save Francis, offering her own life. Delphine brings Francis back to life but the price was Marie de Guise's life.
While celebrating Francis' resurrection with him teaching Mary how to sail on the boat he made her, she decides that she wants her half-brother, James, to become the Regent of Scotland. Eventually Nicholas presents to Elizabeth's offer to Mary. If Mary agrees to the truce, she must withdraw her claim to the English throne. Mary decides to accept believing that it is the only way her country will be at peace. Mary and Francis sign the accord and switch Mary's banners in the throne room to remove the English line. Mary and Francis eventually plan a romantic getaway to Paris. After leaving the French Court, they stop the carriage midway of their trip and go skinny-dipping. After one of their love sessions, Mary goes to back to the carriage to get their lunch but she is grabbed by a band of assassins.
Not long after, Mary begins to scream and quickly is found by Francis. As he fights off the assassins, Mary screams for the guards and is grabbed once again by one of the assassins. She watches as Francis is knocked down and repeatedly beats his head into the ground. She screams for the assassin to stop and gets a knife to her throat. Francis manages to the assassins attacking him and Mary but the last one gets away. Francis then collapses and Mary rushes over to him.
After she tells the guard to bring help, Francis tells her that the time has come. They were meant to be happy but he has another fate predicted long ago. He wants her to make sure that Jean is taken care for and stay in France until Catherine becomes Regent. She promises and he says he sees such beauty and thinks about them as children and their love story, their wedding, their kisses. He wants her to find love again but she never love anyone the way that she loves him. Francis hopes that she does and he then dies. Mary becomes overflowed with grief and is unable to let Francis go until Catherine shows up with Bash, Nostradamus and the guards, having to pull her away from him.
Mary is filled with anger when confronting Nicholas back at the castle. She accuses Elizabeth of being behind the attack to ensure that Mary is a threat if she's dead. Nicholas denies it but Mary ends up tearing and burning the peace accord. She tells him England has taken enough from her. Mary once again emotional, runs into the throne room and tears down the new banners. She then screams out in rage. Days later, Francis' funeral takes place. She learns from Narcisse that the assassins were Scots from a group of radical Scottish protestants who want self-government and Mary's death. She believes that this is Nostradamus' prophecy of her being Francis' undoing and tells Narcisse to hang the assassin. She also realizes that Nicholas was telling the truth. Mary kisses Francis' coffin and is told by the guard that the queen rides in the first carriage as custom. She says she is no longer Queen of France and walks behind the coffin as it rolls away on its cart.
Two weeks late, Mary apologizes to Catherine and gives her back the Queen of France's crown. Catherine doesn't blame Mary and reminds her that she made her son happy. Catherine tells Mary that she is strong and must be for the journey ahead. At the end of the episode, Mary goes sailing on Francis' boat and manages to do it on her own.
While Mary is still mourning Francis in Fight or Flight, she helps Catherine to become Regent. She first looks through Francis' notebooks and discovers that Lord Grenier has been selling off some of his vineyards. Thanks to Greer's help in finding out what he's been using the money for, it is revealed that he has been purchasing mercenary armies for the war in Scotland; profiting off the death of his soldiers. After Mary and Catherine confront Lord Grenier, Mary dissolves the alliance between Scotland and France in order to help Catherine. The soldiers are allowed to return home since France no longer has any duty towards Scotland. The members of the privy council begin to consider Catherine for the regency. Also, Mary makes another hard choice by looking towards the Prince of Spain, Don Carlos to become her next husband.
In The Hound and the Hare, Mary is asked by Don Carlos to participate in a courting game: The Hound and the Hare. Before marrying Francis, Mary had been occasionally hunted by other suitors and because of that she declines. Later, Catherine convinces Mary to change her mind as an alliance to Spain would be a great favor to Scotland. After Don Carlos receives a threatening letter, he informs Mary that he must leave immediately. In order to stop him from leaving, she orders her servants to hide Don Carlos' luggage in the wine cellar. Her plan works and gets him to play the hound and hare game. He happily accepts and tells her his version of the game: the men are the hares and the woman chase after them. They are in the woods and are joined by Catherine, Lola, Narcisse and other lords and ladies. During the hunt, Mary spots Don Carlos but she injures her ankle.
On her way back to the castle, she is helped by Gideon Blackburn. He gives her a warning about Don Carlos and eventually Don Carlos shows her his sex apparatus. He loves pain and has been looking for a potential wife to give it to him. Mary promises to keep his secret but she later tells Catherine. Mary is very uncomfortable to do something like that so Catherine decides to help her out. Late at night, Mary is strapping Don Carlos to the machine and blindfolds him. Catherine sneaks in and begins whipping him while Mary tries talking dirty to him. Don Carlos quickly learns that Mary is not alone and takes his blindfold off. As he lashes out at the women, the apparatus falls over and appears to have killed him. Mary and Catherine run out of the room. Trying to figure out how to cover up what they've done, they go back into the room only to find him gone.
After finding Don Carlos is still alive Our Undoing, Mary and Catherine begin figuring out a plan to cover up their involvement. When Narcisse starts to suspect Catherine on accusations that she poisoned Francis, she calls him out for planting the rat in Lola's bath and tricking him into marrying him. This causes Mary to go to Lola with this information including his affair with Catherine. Lola refuses to believe Mary but realizes that she has no proof and starts to suspect her husband. Mary has another problem on her hands, some barley was stolen by the English troops causing a barley shortage in Scotland. The Scots which include Lola's family that tried to take it back are being held hostage. Elizabeth will only let them go if Lola comes to English Court. After Lola discovers all of Narcisse's treachery, Mary hesitantly agrees to her request to go to England. Lastly, Don Carlos finally wakes up and is revealed to have become impaired, also not remembering anything that happened before his accident. Mary uses his condition as an advantage to save her country and chooses marry him.