In the season premiere, Mary announces to the court that the Black Plague has returned to France. She gives them falls news that they're prepared from the Plague. Before she and Catherine are isolated for their safety, she stops to update her ladies on Lola. Both she and Catherine stay in the court room, in isolation. When music starts playing, Mary asks what it means, Catherine tells her they're playing it to signal someone has fallen ill. Nostradamus comes to speak with Mary and Catherine, volunteering to go find Francis. Catherine is against this but Mary commands her to be grateful and stay silent after she taunts Mary about the reason why Francis left. Éduard Narcisse comes to speak with them about wanting to have a foe killed. He asked Mary to put him in a mass holding cell so he would become infected of the Plague. This blatant demand makes Mary quite angry, as she values every innocent life. He begins to explain how he controls the grain that enters court, essentially blackmailing Mary into killing Pierre Valent. Catherine turns to Mary and tells her this is the real France. Catherine tries to explain to Mary that is the way court works. Mary argues that bowing to the nobles isn't the way to rule. She tells Mary that her position comes from birth but her power comes from nobles. That in exchange they provide the nobles with special privileges. Mary counters that they could simply punish Éduard and claim his grain for themselves. She tells Mary that will only end in a revolt. Mary tells Catherine she wants to be different than other Queens and gives a guard orders to tell Éduard she denies his request.
Éduard returns to the two women and tell them that things have become even more difficult now. Since Pierre and his whole family have isolated themselves in their quarters. He tells Mary that he's going to give her a chance to reconsider and to look outside to see that the villagers are burning the houses of the infected. Destroying the holdings of grain Mary was counting on causing a famine to occur in the land without the grain provided by Éduard. Catherine tries to convince Mary that killing Pierre's family with poison would be kinder than letting thousands starve to death. Soon after, Nostradamus returns from the village to give Mary and Catherine new that the house that Francis and Lola were staying in had been marked with Plague and burned to the ground. Catherine tells Mary that when Francis returns he will thank her for saving the realm from a very naive Queen. Later that night, Mary goes to visit Catherine in her chambers whom looks visibly sick. She tells Mary that she didn't want to become the person she is either; a Queen unloved by her king is hard, she tells Mary not to let Lola get between her and Francis. When she exits the room, she asks Nostradamus how long the symptoms will last since they made her sick, not with the Plague however so she couldn't kill the Valents herself. The next day, Mary walks in on Éduard signalling for the grain to arrive, like she knew he would. She has him arrested for murder because he ultimately had the Valent family and Yvette Castleroy killed. She has him locked in the catacombs where the sick are being kept so that he'll die of the Plague. She returns to the throne room and stares at Francis' empty throne.
In Drawn and Quartered, Mary overjoyed to see that Francis has survived the Plague when she goes to greet him. Quickly walks into his arms and they embrace each other before greeting Lola. She hesitantly asks Lola about the child and she's told by Lola that she has a son, Mary puts on a fake smile. She's introduced to Louis whom she thanks for bringing Francis home safely. Soon after she and Francis retreat to their chambers and have sex. Before Francis brings up the matter of his bastard child with Lola, whom Mary begs him not to claim his son officially. Later that day, she and Nostradamus take a stroll out in the grounds and Mary vows to protect him after he helped her kill Éduard Narcisse.
When she and others are enjoying a celebration for Francis' return, she and Francis are soon pressured by Narcisse to take revenge for Eduard's death by killing Nostradamus. When alone, she confesses to Francis that she indeed was the one whom forced Éduard into the room of the sick. She tells Catherine and Francis that it was her mistake and that she'll fix it before leaving the room. She goes to Narcisse to confess to her crimes and the reasons why she committed them. When there begins to be wholes in Éduard's story as to why he wanted Valent dead. She begins pressing Narcisse with a lot of questions, angering him to the point were shouts that he isn't afraid of her or her husband. He then tells Mary that Nostradamus and the guards whom assisted will be drawn and quartered, to which Mary protests is a horrific and agonizing death. She goes outside with Francis to discuss their options. When Francis tells her she was reckless in killing Éduard, she stands up for herself and tells him that he left her alone to rule a kingdom riddled with Plague. She tries to convince him not to bow to his nobles but to stand for justice. They then decide to find proof of why Narcisse would want Valent dead and why he used his son to command revenge. To do so she goes to Lord Valent's chambers, when she is then interrupted by Lola. They discuss their awkward situation and Mary tells her its alright for her to take joy in motherhood. While talking, Mary finds a letter that showed Lord Valent was desperately seeking an audience with the King before he died. She asks Lola to find out everything she can about Lord Valent's last days.
When Sebastian returns to court, he tells Mary and Francis all about how many people are using the Plague to cover up their crimes. He tells them even Cardinal Morisini was found murdered in an alley. Lola joins in the conversation to tell Mary that Valent took confession with a priest named Father Lucien shortly before his death. She goes to speak with him to ask if he could tell her what Valent told him. He tells her that Lord Valent and Narcisse worked together to collect money for the Vatican but keep it to themselves. Cardinal Morisini learnt of this, so the two of them killed him. Valent began feeling remorse so he was killed. Mary upon hearing this news begs him to testify to this, however since it was said under confession he can't testify to a word. The next day when they are about to kill Nostradamus, Mary stops it and tells Narcisse about letters she found from Valent confessing all their crimes. She's interrupted by Francis who shows her he has the letters. They argue about it before he tells her to leave. Francis joins her afterward and praises her performance in front of Narcisse. She sees Nostradamus off as he leaves court. She then calls Francis to the nursery where she tells him he should claim his son and give him his name before leaving the room.
In Coronation, Catherine is planning a banquet for 1,200 and a huge military parade with new uniforms and amusements. It’s for Francis’ coronation but he doesn't like the expenditures. Mary says it’s shameful and grotesque. Catherine says that’s what she was going for. She says people from all the visiting nations see they are poor and weak, they will take advantage and says their severed heads will be on pikes. Catherine says she doesn't know why Mary is part of this conversation. Francis tells them both to take it down a notch. He says Mary knows she needs to step back until they get grain from Narcisse and the coronation is over. Francis says he’s also negotiating with Ducasse to get grain behind Narcisse’s back. Mary tells Francis she knows she needs to play that part. Francis says if the nobles see that she obeys him, they will too. A man comes out of his tent and calls for quiet so he can hear the spirits speak to him. Francis looks uncomfortable and Mary asks if he has spirits with a message. He says no and goes to talk to Lord Ducasse about grain. Greer and Mary see Louis with another woman and Mary says he moved on fast after Lady Doutzen shipped off to Amsterdam. Mary was thinking he might make a good match for Lola but since they saw him with the courtesan they wonder if she wants a man who pays for love by the hour. Mary sees Francis and asks if he found out about the grain. Narcisse walks up on them and tells them that they can’t harvest because of the after effects of the Plague. Narcisse says it’s really just laziness and Francis says France is starving and asks for a specific shipment date. Narcisse says soon and leaves. Mary tells Francis to take Narcisse’s lands but he says he can’t take him down now. She says they can’t wait much longer. A man is seen running away from a guard however he is killed and Conde checks the basket he was carrying which contained a chicken and some bread as the man was just trying to feed his family.
At the ball, Mary and Francis meet Ducasse, his wife, Monique, and their son, Guy. Francis asks about the grain and he says it’s ready to ship but says other nobles make excuses when asked for grain. He says Narcisse brings down any who oppose him and says he has a long reach. Francis says he will protect him. Herr Shuler comes to see Mary and asks her to have Francis release German prisoner and says he will give grain in return. Mary tells Francis that the Germans have grain and he just needs to let the Protestant prisoners go and says the Germans aren't afraid of Narcisse. Francis says this is not a good week for that because it wouldn’t please the Catholic nobles. Later, Mary and Francis find out that Ducasse changed his mind and know Narcisse is behind it. Mary reminds Francis of the German offer. He says he can’t let the prisoners go without investigating their crimes. She says there are two days. When Francis goes off to tent city on an errand, Mary goes and tells Schuler that Francis is intrigued by his offer and needs time to consider. He asks if he needs to talk to the king directly. She says he can deal with her. He says he’s leaving and that his friends were jailed for their faith nothing more. Mary talks to Greer about the German problem and says they can’t find Francis and the Germans have the only grain they can get. Mary chases Shuler down and says the kings guard will take them to where the prisoners are being held. He says she’ll have her grain and he thanks her. Mary tells him that she freed the prisoners and says there was no time. She says Shuler was leaving and he had disappeared. She says he offered a fair deal. Francis says she has ruined him on the eve of his coronation. She tells him to tell another story. He says that she did it, not him. He says this is about his legitimacy and filling the shoes of a man they feared. He says the nobles won’t respect him if his own wife won’t. She offers to help but he says no more help from her.
The next day, the German Duke rides up as Francis and Mary watch the amusement. Shuler says the German prisoners are missing from the garrison. He says they were moved two days prior. Shuler shows them implements of torture he took from the garrison. Bash reminds him he’s talking to the King of France and Shuler says he’ll find the prisoners himself. Bash calls the guard to arms and they surround the Germans and it’s a stand off. Francis tells them all to put down their weapons. Francis comes to Mary and says this has stirred up all the hate. He says he spent an hour smoothing things over with the Germans. Mary says there is time to fix this and says they need to find the prisoners. She tells him he needs to maintain a delicate peace and she will clean the mess she created. Mary brings some of the garrison guards to her and asks where they were taken. They said they went to to a tavern and admit there was a whore who offered herself to them one after another. He says her eyes were remarkable. They describe her eyes, one green, one blue. That lets her know that Louis took them. He says his love’s ship was taken by the Germans. He tells her that his ship was taken because of old hates that Henry inflamed. He says Francis is ruling the same way. Louis says he promised Doutzen safety and she tells him he’s a better man than that. She tells him to bring the prisoners back to the castle and he says he has to do everything in his power to bring back his love. She says men should put country before love like the king does. He says he’s not a king and glad for it and rides away. Later, Mary brings Francis to the balcony to show him the returned prisoners. Louis bows to them. Mary says they don’t need Narcisse anymore.
Francis calls Narcisse who says it’s a great day and Mary tells him the Protestant prisoners have been found and traded for grain and the cause of religious tolerance. Francis says he understands that Narcisse would like teach him how to rule. Francis says a king must make new friends. Mary tells him not to lecture her husband on betrayal since he betrayed the promise to deliver grain. He asks if Mary speaks for the king and Francis says she is his Queen and speaks in most things. He tells him he will need a friend soon and if he doesn't bow to him, he’ll learn that. Narcisse bows to them, calls them majesties and says grain will arrive today. Francis and Mary are pleased. Mary meets with Louis and thanks him for returning the prisoners. He says he wanted to be the better man she saw in him. She says as part of their new understanding with the Germans, Lady Doutzen will be returned home. He thanks her and she says he has Francis to thank and says he negotiated it. He says the Lady isn't coming back to him, but to her husband. He says she has children and the man is a good father. He says she’ll discover that bond when she and Francis have children. Francis walks into his coronation and says he was wrong to ask Mary to step back. He says they are better together as equals. He says this coronation is for a King and Queen.
In The Lamb and the Slaughter, Mary, Francis, Catherine, and Lola converse in the ballroom as it is being set up for the celebration of Francis claiming his son. Mary asks who Lola has chosen to be her son's god-parents, she gets a response that they have yet to choose. She's told by Catherine before she leaves that she's doing well by avoiding the whole thing since most Queens wouldn't attend the christening of their husbands bastards wither. Mary follows Lola as she leaves the group in frustration. After discussing the whole situation the three are in, frustrated with Lola. Mary chooses to release her from being one of her ladies in waiting. Later that day she's found by Francis outside. She begins to reminisce about their time together in the castle when they were young, before announcing to Francis that she is with child. The two embrace each other in a moment of complete happiness and bliss. Catherine later walks in on them in the middle of having sex. To celebrate the fact that Mary is finally pregnant, for which she announced was hoping was a son. When they tell Catherine they wish to keep the news a secret for now, she replies telling them that this will make Mary's claim to England stronger than ever. She then announces the news to Greer, Kenna, and Lola. The four share a toast of champagne in Mary's honor.
Both Mary and Francis are later approached by Lola who relays her concerns about Estelle and Narcisse's marriage. When Lola's concerns about Estelle begin to sound a lot like those for herself, Mary kindly asks Francis to leave them alone. Mary tells her that she understands her concerns, as she has felt like her life wasn't in her own hands before. Lola replies by telling her that she and the other ladies did all they could to help her. That she fears Mary's happiness has affected her ability to be compassionate. Mary in an angered tone tells Lola that she's been nothing but compassionate for her. That Lola's "cage" was of her own making when she decided to sleep with Francis. The argument heats up from there, Lola turns her back to Mary. Still in a state of anger she tells Lola it would be best for her to be housed elsewhere for she doesn't want to have her in sight. Later that night at the banquet before the christening, she looks for Lola. Letting Francis know that the two had an argument and it went too far. She joins Condé to discuss the matter of Narcisse and his possible brutality towards his former wives. They are interrupted by Catherine whom asks Louis to dance with Greer to get the people dancing. She then makes her way to Narcisse, to question him about his marriage to Estelle. In efforts to release Estelle from the marriage, Mary tries to nudge Narcisse into getting an annulment since they have yet to consummate the marriage. While talking, they are interrupted by a man who brings news that Estelle is missing and the guard at the door has been stabbed. Mary goes to find Lola in her chambers, where she finds her helping Estelle clean blood of herself. After arguing with Lola, she agrees to help get Estelle away from court. Right after she ushers Estelle into a carriage, one of Narcisse's guards questions her about whom is inside. To stop him from checking, Mary delivers a direct threat to the man. When she and Lola return inside, she's asked why she helped get Estelle to safety. She replies to Lola that she was in danger and is her friend. She asks Lola to stop feeling guilty and stay with the people she loves. Mary is asked to be the god-mother of Lola's son to which she accepts.
The next day, while asking Francis is he's alright with Mary being the god-mother of his child. He replies that it makes him happier than a King has right to be. When she begins to feel pain, Francis grows concerned. She tells him everything is okay, she just forgot the gift for the baby in her chambers. A concerned Louis, asks Mary what's wrong and she asks him to help her to her room. He points out that there blood running down her leg, to which she replies that she's losing her child. She begs him not to tell anyone that she's had a miscarriage. Because she wants to tell Francis herself and doesn't want to interrupt the christening. At the christening of John Phillipe, Mary as his god-mother holds him as the priest marks a cross in holy water on the baby's forehead. Later, while in her chambers she's found by Francis, she tells him he lost the baby. Francis comforts her while she lets her emotions take over her. Later that night, she's asked by Francis to join him on the balcony. They again reminisce about their childhood. He opens the windows to show her lanterns floating in the sky for her. He holds her in his arms as she cries and tells her, "Whatever the future brings, you are my light."
In Blood for Blood, Mary asks Francis what he was really doing instead of playing dice with Bash since she could tell it was a lie, she's told that he was visiting his son. When he tells her he didn't want to tell her because its a sensitive subject, Mary tells him she isn't a porcelain doll. She asks him not to tiptoe around the subject of the miscarriage, that its making her think he's lost hope. Just as the two are about to kiss, they are interrupted by Sebastian and Leith, who tell them there has been an attack on a Protestant service. Later, she and her ladies take a stroll in the ballroom as its being prepared for Greer's wedding. When Greer asks her how she's feeling she replies that her wedding is a welcomed distraction. She soon after goes to find Francis to tell him he's requested in the throne room to learn more about the attack. He asks Mary to go for him and that he'll join her later. Mary deals with the requests for justice by the Protestants who were attacked. She notices Condé looking noticeably distressed and when she asks him what's wrong, he replies to her that the boy who was killed in the attack the Protestants brought was his nephew. She later finds Condé to tell him that Francis won't release the men who killed his nephew. He starts to explain about how this could have been a planned attack on his family. When Mary questions it, he shows her the mark of the riders on his shoulder. They continue to discuss about The Riders and the tension between Catholics and Protestants.
She later accompanies Louis as he interrogates the men who killed his nephew. She pulls him off a man after things get heated. She then takes over the interrogation with a nicer approach. Mary gets one of them to confess to what exactly they did. Later that night, Mary finds Francis to again discuss the issue of religion and attacks. They decide to have religion neutral justice for crimes and that the Catholic men will be hanged. However the next day, she's unexpectedly told by Francis that he has decided to release the men rather than hang them. The two argue over the issue further when he says "my people" instead of "our people". Mary infuriated, tells him that he told her they would rule together. He tells her that he can't always be her husband first. Mary knows something is wrong since he's acting out of character and she begs him to tell her but he just walks away. She then goes to the ballroom, to attend Greer and Lord Castleroy's Wedding. Later after the festivities, she retreats to her chambers, she again tries to figure out Francis would let murderers walk free. After arguing more, Mary asks him if he worries that she can't have children. He tells her that yes, he wants heirs and her failure disappoints him beyond words. Mary is heartbroken and saddened that the truth would be that he's lost hope.
In Three Queens, Mary jumps at the opportunity to get out of the castle when she hears that Catherine is taking a carriage to a noble's party. Catherine claims that making an appearance at such an event is always a good idea. However, once inside the carriage, Mary quickly realizes they're not going the right direction. Apparently Catherine is going to give a speech thanking a village for its love. Their carriage ride is interrupted by some royal-hating folk, Catherine reveals one of her many secrets to surviving the royal life: Always have an escape hatch in your carriage. Mary and Catherine quickly escape and remove their jewelry in order to look like commoners, and luckily for them, nature is feeling helpful today. After Catherine steps in a fox hole—which she claims is a badger hole because her feet are "too dainty to get caught in a fox hole"—Catherine and Mary limp their way to the nearest village. Once there, Catherine tries to trick a man into giving them dinner without seeing coins first. Mary tells the man the she and her "mother" are lady's maids who are willing to work for food and a place to sleep. But thanks to Catherine's ankle, Mary is left to serve drinks and milk goats on her own. Soon after, the women are served dinner. When Catherine asks why Mary wanted to come with her on the journey, Mary finally fesses up that she was planning on seeing a physician with "knowledge of women's problems." Mary's fertility issues. However, Catherine thinks that Mary's bigger issue is her "foolish romantic expectations" for her marriage. As someone who has walked the same road Mary's currently walking, Catherine advises her to give up her dream and accept the distance between her and Francis. And if the crown weighs too heavily? Line it with velvet. It's what Catherine does.
Catherine and Mary when they're introduced to Mary and Francis impostors, who are doing their best to stomp all over Mary and Francis' reputation by burning down farms, collecting money, and just generally telling awful stories about Catherine. Mary goes to the girl playing the queen, and together, she and Catherine convince her that they too are "tricksters." And in exchange for Catherine's crown, she gives Mary and Catherine for a ride to the next village. A fake guard named Griffon appears and takes Mary, Catherine, and the female impostor in a carriage but is set on burying Mary and Catherine. Mary and Catherine discover his true intentions and luckily has her dagger on her. Once they're brought out of the carriage, Gifford reveals that he was paid by Elizabeth to set up the impostors. Turns out Elizabeth isn't happy with Mary's decision to wear the English coat of arms. Soon after that reveal, the female impostor stabs Gifford but not hard enough. He breaks her neck instead, and Mary does the only thing she can think of; poke the horse's behind, thereby forcing it to kick Gifford in the face and crushing his skull.
Francis and his men arrive soon arrive. Back at the castle, Francis helps Mary off of her horse. He tries to talk to her but she is tired and returns to their chambers. Soon after, Francis says he was scared of losing Mary today and tells her he didn't mean the words he said. He says he can’t live this far apart from her. She asks why he’s afraid and says she’ll stand by his side no matter what is going on. He tells her she doesn’t have to be so ferocious and says he was just feeling the pressures of being king. He tells her he will never leave or betray her. She says lack of honesty is a betrayal but he says he will fix this. She says she believes him and he asks if she means it. He asks if she’s acting the dutiful wife and she says no, she would never do that. He hugs her and buries his face in her neck. She looks sad because he’s still not being honest with her.
In The Prince of the Blood, Mary is working and having breakfast with Kenna and Lola. Francis comes in and sits at the other end of the table, Mary tells Kenna and Lola she’s sick of him keeping secrets and bowing to corrupt nobles. Narcisse comes in and has an edict he wants Francis to sign saying all residents have to come forward and state their religion. Francis asks why they are pushing it and Mary says it will call bloodshed in the streets. Narcisse says Protestantism starts with the commoners and by the time it spreads to the nobles, it will be too late. Bash interrupts and says Claude has arrived. Mary is surprised Francis’ little sister is there and Francis says they must go greet her. Out in the halls, Francis introduces Claude to Mary who asks if she remembers her. Claude says she seems so tall in her memory.
Mary sees Greer and runs to check on her. She has a cut on her wrist and she says they were traveling through Orleans and they were attacked and robbed. She says they barely made it back alive and begs Mary not to tell anyone. Mary tells her to tell her the truth. Greer tells her they were attacked in Orleans because Castleroy didn't take mass. She says the church came after them. Mary asks if she married a Protestant and Greer says she did but hasn't converted. Mary tells her about the law the nobles want signed to identify the Protestants. Greer is shocked and says they’ll be persecuted. Mary says she’ll try and persuade Francis not to sign it. Mary goes to Francis to talk about the edict. She says she knows they are on the same side when she saw his reaction to the edict. She tells him to take a stand. Francis says he may not have a choice. He says he’s the Catholic king of a Catholic nation and says he has to take this into consideration. She tells him the edict is wrong and he knows that in his heart. He says there are limits to what he can do as king. He tells her he will handle it on his own in his own way and asks her to be patient. She agrees. However, she goes to see Louis and tells him she needs his help since her husband isn't giving her what she wants. She tells him about the edict as they walk and she says the nobles are too strong to oppose when they’re united. Louis wonders why Francis isn't listening to her and asks how he can help. She says they need a Protestant noble to openly oppose the edict. Mary says there are other nobles that have converted to open the dialog. He says whoever does this risks everything. She asks him to bring her a Protestant noble in private to talk. She says if they don’t speak up, the edict will go through and they will still be in trouble.
At the party, Louis points out Lord Cane to Mary, a Protestant. Mary and Catherine watch Louis and she says he’s a Prince of the Blood and the Bourbons were once rivals for the throne. She says the Bourbon princes were once in line if she couldn't produce a male heir. Cane tells Mary she’s asking him to be a martyr but she says it’s time to come out of the shadows and let Francis know there are Protestant nobles that will stand with him. He asks why she’s helping and she says she has friends who would share his fate. He says he has to sleep on it and will give her an answer tomorrow. The fireworks start and Louis tells Mary she’s daring and fierce. She says she has to be until others are the same.
The next day, Narcisse asks Francis in front of everyone to sign the edict and says all the nobles are in support of it. Cane is too scared so Louis steps in, admitting that he is a Protestant. He says he stands there to tell them that the Protestants of France are not his enemy. He asks Francis to stand on the right stand of history. Then the other men join him. Louis asks Francis to take the time to think more about this law. He tells them no one must harm these men for coming forward and says he’ll think about the law some more. Mary tells Louis he was brave and he says he did it for her. She tells him he has her gratitude. Mary goes to stand by Francis. He tells her he knows she had a hand in this and she says she wanted to give him the chance to do the right thing. Mary finds Greer who tells her Francis signed the edict. She goes to find Francis and argues with him. He says he realized he needed the support of the nobles. She calls him a liar and a coward. He tries to tell her he did this for her. She says she waited for the man she loved to return but that man is dead. He tells her if that’s what she thinks, she should leave him and return to Scotland.
In Terror of the Faithful, Mary denounces Cardinal Vasari and blames Francis for ratifying the edict and he compounds that by refusing to take care of the men himself; he wrote a letter to the Pope requesting that the inquisitors be removed and, he argues, taking matters into his own hands would defy the Pontiff and turn the Vatican against France. Francis once again suggests that she return to Scotland. Mary tells him that while she may have decided to give up on him, she's not giving up on France. Later, Mary and Francis are told by Louis that the minister wants to rebuild the Protestant church. Mary encourages Francis to grant the request and says it could imply they have some protection. Francis gives the minister permission to rebuild and says that’s all he can do. The minister says it’s not enough. He says they are being hunted by the Vatican. He tells Francis he has two days to expel Vasari and the Inquisitors or else Catholics will be attacked in retribution. Francis doesn’t like being threatened and has him arrested. He says he’ll get the truth out of him about where the arms and explosive they have are hidden even if he has to beat it out of him. The man is taken away and Louis apologizes and says he didn’t know the man was a fanatic. Francis asks for names of some of the others but Mary says this was inevitable. Bash and Condé set off to discover where these explosives are. Once again, Mary and Francis are left alone, and Francis pretends he cares not for his wife's opines.
Francis and Mary send Lord Girard off kindly and Mary says acting normal feels strange. She says she doesn’t know which is harder, pretending there’s not an attack coming or that their marriage is well. Louis shows up and says the attack is the work of a few fringe radicals and says the Protestant leaders really don’t want this. Francis goes to the dungeon to talk to the minister. Mary walks with Louis and asks why the Protestants would send their minister to be tortured and killed. Louis says the people don’t know about his threat and that if they kill him, it will create a martyr. Mary begs him to try and talk sense to Francis and Louis tells her Francis is a fool to ignore her wisdom. Francis has the man on the rack being stretched and tortured. The minister says he put the bomb there himself and then says they must have lied to him. Francis demands his co-conspirators names and has him stretched again. Mary comes in and tells him to stop. He tells her to go away and she says they can’t martyr the man – it will make things worse. He has them stop and pull the man off the rack. His arms are dislocated and they pop them back in. It may be too late for the minister. Francis tells Mary he never meant for any of this to happen and hopes she knows that. Bash returns to the castle to tell them what has happened, when they hear that in the town center the minister has been crucified upside down. 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, and that she is forever disappointed in him, with the cutting words, "I have lost all faith in you, and the man I thought you were."
In Acts of War, while her ladies and Claude are talking about Narcisse, Mary comes up with the idea of marrying Claude off to Condé and proposes the idea to Francis. The marriage will send a message about Protestant acceptance. She says he would exemplify tolerance but he says the nobles would rise against them. She says it would give the Protestants no real power. He says no and she says she expected that answer. Later, Francis agrees to Mary's idea and tells her to go talk to them both because he would rather they agree than him force the marriage on them. She agrees but says not to go back on his word and informs Condé of the matter. He hesitantly agrees to it and then she meets with Claude. Catherine shows up and says she won’t have a Protestant or a Bourbon marry into their family. Claude refuses the marriage and Catherine says it’s a miracle they can agree on it. Mary says if the king wants it, it will happen. Claude stomps out and Catherine says she needs Claude married off an away from court. She threatens Mary if she toys with Claude’s future.
That night, Mary says it all seems to quiet and Kenna says it’s hard earned after the strife but Mary says it won’t last. Condé asks Mary if they should wait for Francis to come back to announce the engagement. She says no and says she believes in Francis no matter what. She says the best marriages are based on certainty and faith in the other. Mary claps her hands to get attention. She says with the king’s blessing, she’s announcing the marriage of Francis’ beloved sister, Claude, to his good, friend, Louis Condé. Later, Gerard and other fake guards hold Mary hostage, threatening to kill her but instead she is raped by Gerard. Mary manages to escape and sees Catherine down the hall. Catherine takes Mary to her chambers and asks about Francis' whereabouts. Mary tells her they came for Francis and when they couldn't find him they attacked her. Catherine realizes Mary was raped. Mary cries and slumps to the floor. Catherine says she’s safe and says she is alive and will survive. She says she knows this because she survived it too. Catherine says no one can take your proud. She tells Mary they are going to change her clothes and fix her hair and erase all mark that it happened. Catherine says they tried to diminish the king by degrading a queen but they won’t succeed because no one will never know. Catherine says she’ll walk out with pride and ignore that it happened. Catherine says she has to act now to make sure she’s not seen as a victim. She tells Mary to not let them win. She tells Mary to trust her and let her help. She holds out her hand and says she can get her though this then Mary takes her hand.
Mary walks into the throne room with Catherine. Mary takes the throne and Catherine stands at her side. Mary tells them that she and Francis are safe and the invaders have achieved nothing and will die for nothing. She holds back tears and Catherine stands there to reassure her. Catherine tucks Mary in and she says she’s cold. Catherine tells her it’s shock. Francis comes in and Catherine tells him to give Mary time and space and leaves. Francis says he heard she was untouched but Mary tells him that was a lie. She reveals to him that she was raped. He tries to walk over to her but she tells him not to come any closer. He says he loves her and this is his fault. She says she knows he was doing all he could to right things and says he can’t blame himself but it hurts to speak and she doesn't want to talk about it or make sense of them. She tells him to find and kill the men who did this to her.
Mary spends her time looking for her attackers in Mercy. After Francis promises to hunt the men who hurt her, he reveals the the truth to her about why he's made the choices that he made. He tells her he was being blackmailed by Narcisse for killing Henry at the joust. Henry was a threat to her and France and it’s regicide, also Francis said that she needed to be able to deny any involvement and continued thinking he would find a way out. Mary reveals to her Kenna, Greer, and Lola that she was raped and she joins Conde to find her attackers. They eventually find them and Conde kills most of them men while Mary confronts the man who raped her. She tells him he’ll hang and says she’ll be remembered for hundreds of years while he is dead and forgotten. He says God will grant him pity and she throws a lamp at him setting him on fire. The next day, Mary tells Francis that her attackers are dead. She cries as he sits next to her and tells him that they can’t put the pieces back together. She says she can’t change the fact that she blames him. She says she knows it’s irrational but says her rape feels linked to him and them. Francis says he was trying to save her life and asks how telling her could have changed things. She says she doesn't know if it could have gone differently or better and now they’ll never know because he never gave her the chance. She says they need to lead separate lives from now on and says she will lead with him but will be his wife in name only. He refuses and says he won’t live like his parents. He tells her he loves her and knows she loves him. She says – look where that love has brought us.
Mary continues to spend time apart from Francis in Getaway. When he brings her firewood, she just wants him to leave her alone. She wants to get away and visit their chateau. When she hears from the Cardinal that Conde is wearing the brand, she takes Greer and Leith to Conde’s estate, and helps him escape out the window and to her carriage, before the Cardinal’s guards can take him. Mary, Greer, Leith, and Conde arrive at Conde’s brother, Antoine's home. King Antoine welcomes them and talks Mary into staying for the night, and attending his party as the guest of honor. When things start to get too sexual at the party, Mary and Greer leave.
Greer assumes that Mary is upset by the improper party they’ve left but she’s not over everything that happened to her, and can’t stand even a simple courteous touch from a man. Greer promises she’s strong and she’ll recover. Mary feels like she’s sleepwalking and cries as Greer hugs her. When Mary is preparing to leave for her chateau, Conde comes to say goodbye. He tries to talk her out of returning to France, since her husband’s decisions have endangered her. She argues with him as she doesn’t trust his advice on the matter since she found his letter the Conde leaves. The Cardinal’s guards arrive at King Antoine’s estate, for Conde. Mary decides that they need to burn off the mark of the Dark Riders in order to create enough doubt to have Conde arrested and taken back to court, where she’s certain that Francis will intercede on his behalf. Leith heats the sword, while the guards are at the door. As Leith burns the mark, Mary grabs Conde’s hand and offers comfort while he screams. They go the Cardinal's guards and claims it was a wound that had to be cauterized after a drunken sparring match with the captain of her guard. As Mary and Greer head back to court with the Vatican transport, Mary tells Greer that she was able to touch someone and connect and doesn’t want to be distant anymore, including from Francis. Finally back at the castle, Mary goes looking for Francis, and finds him asleep on a nursery bed, with his son and Lola. She looks deeply hurt and leaves without waking him.
In Banished, Mary is confronted by Francis to why she is still avoiding him. She tells him she saw him, when he was asleep with Lola and their baby. She says he doesn’t need to explain but it still hurts. She also rebuffs his touch, telling him she’s still anxious being near any man. Mary receives a report that a man being questioned in the dungeons identified Castleroy as being one of the people who funded the attack on the castle. When Mary questions Greer, she denies that there could be any link between Castleroy and those men. When Conde arrives, he plans to refuse the estates that are being offered Protestant lords. Mary tells him that it’s all been more complicated politics than he realizes but he doesn’t want to hear her defend Francis anymore. She puts her hand on his arm to detain him which Francis sees from afar but he storms away. Later, while Francis and Conde are having a duel, Kenna realizes that the men are fighting about Mary. Francis wins the duel and Conde continues to try to go after him but Mary and the guards stop Conde. While Mary’s treats Francis’ cut face, he tells her that he knows Conde wasn’t just provoked by his issues with Francis as a ruler. Conde has feelings for Mary and she asks him if she thinks she somehow encouraged Conde, when she can barely stand the touch of any man, even her own husband. He tells her that he doesn’t want to bring it up, given what she’s been through, but when they produce an heir, there can be no doubt about the paternity. Mary knows her head would be on the block if there were. Mary asks Lola to offer herself as a potential match for Conde. During the party, a guard arrives with Castleroy’s ledger, claiming it contains proof of his guilt. Mary goes to see Greer in the dungeons as Castleroy's ledger is enough to convict her. Mary spares Greer's life but rips her of her title, holdings, money, and her rooms and position at court. Francis goes to Mary and is sad that she’s lost Greer and can no longer be friends with Conde and feels alone. He asks if he can stay with her, sleep on the couch and just watch over her while she sleeps.
In Sins of the Past, Francis suggests to Mary that they get away to an abandoned chateau in the Lore Valley. Mary thinks they can afford to give Navarre a little money but Catherine vehemently disagrees. Catherine and Francis believe the Bourbons have always been trying to further their claim on the throne, since Francis was a sick child. Later, Mary hears Catherine screaming and runs to her chambers to find Catherine hallucinating. Catherine believes her vision to be evidence of the truth of Nostradamus’ prophecy but Mary and the others believe that she is ill and needs rest. During the night, Mary thanks Francis for his efforts to make her happy, not just the new chateau, but sleeping on the divan night after night, until she’s comfortable. She tells him that he can sleep on her bed, just to sleep. Mary begins to have awful flashbacks from the sound of a man’s breath next to her in bed. Francis tells her it’s a nightmare, one that’s over now. Francis holds his arms out and she walks to him, letting him hold her as she cries.
The next day, Mary dances with Francis at the Winter's Ease Feast. Lola observes to Conde that Mary looks happier than she’s seen in a while. Narcisse drags Francis and Mary from the ball to tell them that Navarre is poor and does need help with their Protestant refugees, but that the help has already been offered by England. Rumors are that English troops will arrive to assist in Navarre. Mary and Francis try to deal with the idea of English troops being that close to France’s border. Mary asks Conde to spy on his brother and he becomes angry with the idea especially believing that she is taking advantage of his feelings for her. Later, Mary wonders what they can do to convince Elizabeth that she’s not a threat to her. Francis says there is no way, and they’re back to Mary feeling tormented and unsafe. She tells him that she wants him to be free. He doesn’t want that, asking how could she send him to another. She tells him it's because that she loves him and one of them should be happy.
In The End of Mourning, while sledding with Lola and Kenna, Mary sees Lola and Conde sharing a moment and starts to look a bit jealous. Conde asks for Mary's permission to take Lola to his estate so that he can get to know her a bit better and Mary allows it. Back at the castle, she is reunited with her uncle, Christian de Guise. He has come to be the king's magistrate again despite running that he ran away quickly as soon as the Plauge started. He warns Mary that the Bourbon brothers are a threat to the throne. Francis asks Mary to make Conde stay for a dinner party in order to find out if he is guilty of poisoning Henry. Mary gets Conde to stay but also calls off his courtship with Lola. Francis realizes that she let Conde think it was because she has feelings for him. Before they can continue their conversation, Bash comes in and informs them that the valet they were seeking was killed in Conde’s region shortly after leaving court. Francis decides they have to confront the Bourbon brothers directly, and if Conde’s guilty, he’ll have to be beheaded.
During dinner, Conde is angry at the accusations made towards him and it is revealed that Mary's uncle was the one who poisoned Henry. Mary goes to see Conde to apologize to him but he is angry with her for lying to him. The next day, Mary writes a letter to her mother, to inform her of the Duke’s fate. Francis wishes they’d known about the poison sooner, so that Mary could have been spared all this. He siggests that maybe they can still salvage the match between Conde and Lola but Mary thinks they should step back instead of trying to force other people’s hearts. Francis says he can’t move on to another, as she told him to, because his heart is closed to anyone but her. Mary seeks out Conde on his balcony and tells him that she would never betray Francis. She has nothing to offer Conde and leaves.
Mary is reunited with her mother in Forbidden and is being pressured by her to conceive an heir before Elizabeth secures her country. Mary admits to Francis that her mother is right about them needing to produce an heir. He thinks it’s too soon and not a good enough reason to be together, if that’s not what she really wants. During the night, Francis is escorted to Mary's chambers and she tells him that she's sure, making the first move. After a few kisses in bed, Francis pulls away and Mary tells him that an heir needs to be conceived to secure her place, if they go on to separate lives. He wants to know if she has feelings for Conde or if she just wants to secure her rule in Scotland before she turns to Conde. She tell him both and he forbids her from being with Conde. Later, Mary tells her mother there will be no heir because she was raped and that’s why she and Francis no longer share a room. Her mother is far from appropriately sympathetic. Mary tells her that she realizes now that she is her own person, and utterly alone, but perhaps better for it.
Outside, Mary sees Conde and he knows that Francis is suppose to be with her. Mary confesses the plan was a failure because she froze and couldn’t go through with it. He tells her to be patient with herself. She tells him not get his hopes up about this, because Francis has forbidden them to be together. She finds out from Conde that her mother drugged Lola. The next day, Mary confronts her mother who admits to drugging Lola and reveals that she is dying. Mary wants her to stay at the castle and be cared for, but her mother insists on returning to Scotland. Mary tells her not to worry as she will not let anyone take her country from her. At the end of the episode, Mary tells Conde that she wants to be with him and would like that he come to Scotland with her.
In Tasting Revenge, Mary continues her romantic pursue of Conde and tries to distant herself from Francis. By the end of the episode, Francis allows Mary to be with Conde if that will be able to heal her
In Tempting Fate, Mary finds out of Conde's betrayal of him courting Elizabeth. With Lola's advice, she forgives him and sleeps with him.
Mary hears of Francis' collapse in Reversal of Fortune. Catherine unleashes her fury on Mary for not being a wife to her son and planning to abandoned him. Catherine believes that Nostradamus' prophecy has come back into play and tells Mary that she never thought she would kill Francis by breaking his heart as the last thing he heard was of Mary running away with Conde to Scotland before he collapsed. After Catherine leaves, Mary begs an unconscious Francis to live. Mary tries to deal with the nobles from finding out of Francis' condition and the Protestants staging a coup. Mary feels against using Francis’ troops to save Scotland but Lola and Conde convince her that it’s necessary to save their home and families, and also to save her crown. Conde reminds her, should anything happen to Francis, she loses her French throne. Catherine barges in and makes Conde and Lola leave. Catherine snaps at Mary, telling her that Scotland is lost and do not drag France down with it. Catherine knows Mary has the authority but will do everything in her power to stop her.
Mary hears that Narcisse has a private army and commands him to hand them over. Later, Mary demands that Narcisse be sent to the dungeons for defying her with Renaude’s army. She confesses to unconscious Francis that she’s sent French forces to Scotland even though she knows he wouldn’t approve. As she cries and begs him to live, he wakes. The next day, Francis has made his decision to send two-thousand troops over to Scotland as he feels confident France can handle it. After Catherine leaves, Mary wants to know why he's doing this. Francis feels strongly about the promise his country made to ally with hers but he doesn’t plan to give her anything else, including his trust ever again. Mary goes to Conde and chooses not to go back to Scotland and stay by Francis' side. She can’t weaken Francis in the eyes of everyone, when he’s already weakened France to protect the alliance with Scotland. She returns to Francis's room and watches him sleep.
In Abandoned, Mary meets with Conde in the forest and tells him that she still cannot leave France and proclaims her love for him as she still wants to continue their relationship. However, later in the episode, Conde betrays Mary by marrying Elizabeth after still refusing to escape to Scotland with him.
After confronting Conde about his betrayal, Mary still continues to help him in Fugitive. However, after Conde's capture, Francis lashes out at Mary when finding out from General Renaude that she tried to help Conde escape the French Court. Conde had escaped thanks to Elizabeth's men and now he can claim Francis' throne meaning the end of Mary and Francis' reign.
During The Siege, Conde tries to start a war with Francis unless he surrenders the throne and many lives will be spared including Mary. By the end of the episode, Mary goes to Conde and tells him that she is pregnant with his child.
Mary's plan is revealed in the finale. As Mary stays with Conde at the camp, a ruckus starts outside. Conde’s men appear to be coming down with the Plague because of one of camp prostitutes goes about screaming about it. Conde realizes it's a hoax and when he confronts Mary, she stabs him. She says that she never wanted to hurt him but she had to stop him.
Later, Bash tells Francis that Mary gave him a package for Greer before she left and maybe something is up. Francis insists now is the time to lead an attack even though Conde’s men still outnumber theirs. Francis finds Mary next to a bleeding Conde. Mary tells Francis that if one of them was going to die, it couldn't be Francis. In the end, Mary chose Francis over Conde as he is still her husband and she has always loved him. Back at the castle, Mary has a moment with Francis and thanks Greer for her help. Francis has decided to not execute Conde turn him over to his brother as long as he no longer continues to claim the throne.
Mary sees Conde in the dungeons and he realizes that he couldn't compete with Francis. She then finds out that Conde had Jean kidnapped to use as leverage against Francis but the plan failed and Jean was killed, causing Francis to change his decision and have Conde executed immediately. Mary goes to comfort Francis and Narcisse comes in, wanting permission to find Lola whom has gone missing. He believes that someone in the castle had something to do with the plot and wants them to keep his search a secret.
Later, Mary finds that Conde has escaped from the dungeons and that the executioner and guards have been killed. Bash updates Mary that the king’s guard is after Conde, and they know that the fake executioner was English. Narcisse tells Mary Lola and Jean are alive and unharmed. The baby’s death was a ruse meant to hasten Conde’s execution. Mary immediately jumps to the correct conclusion of the whole thing being Catherine's plan. Mary confronts Catherine over the proof they have of her terrible plot and yet she feels no remorse for what she did. Catherine claims that Conde signed his death warrant when he had an affair with Mary. Mary intends for Francis to know what Catherine has done. In the throne room, Mary watches as Francis exiles his mother from the French Court and rips her of her titles and money.
Later, Mary says her goodbyes to Kenna after arranges for her to stay with a couple who will adopt her baby. Mary goes to meet with Francis in her chambers. He told 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 and he believes she’s proven that. She wants to know if they could recommit to each other and love each other again. They begin to kiss and eventually end up in bed. She tells him she’ll love him for the rest of her life and she'll never let him go again.