In the season premiere, Francis rides to the cottage where Lola is staying, on the way he passes people who are infected with the Plague. When he arrives at the cottage, Lola tells him that he has a son. He and Lola begin to discuss what could have happened, he tells her that he resents her for not telling him about the baby. She states that he hasn't touched the baby and its alright if he doesn't want this, that the child will have Lord Julien's name. When they realize that a young boy named George who resides in the house has the Plague they quickly go outside and they prepare to leave. Before they leave Estelle, tells them to lie about who they are because the village won't be safe for the King. When on their way to a river so Lola can drink water and feed the baby, they run into Louis Condé, Francis' cousin. Francis again, asks her why she couldn't have just told him the truth. She tells him that she wanted to handle it herself to save him and Mary the trouble. She tells him she could still leave with the boy and no one would know but Francis tells her he's the king and that child is who he says he is.
They are later joined by Stéphane Narcisse who brought Estelle with him caged, until they determine if she has the Plague or not. When he leaves them, Condé tells Francis that some nobles work hard or serve the crown but others such as Stephane take short cuts to power. When Stéphane blatantly mentions Condé's ship leaving France, knowing Francis' wouldn't know about it. He tells him suggestively to know who his real friends are. After Francis is advised by Condé to send Lola to The Netherlands with the ship so she can lead a normal life, he tells her to do so. He tells her that he must return to Mary. The next day after he holds his child for the first time however, he is overcome with regret from his decision to send Lola and his son away. He then changes his mind and tells her she can't leave on the boat with his son.
In Drawn and Quartered, Francis returns to court with Lola and his son and is greeted by Mary. He quickly asks Sebastian to be a member of his privy council, he then introduces Condé to Mary before he and his wife retreat to their chambers and have sex. After they discuss the idea of Francis claiming his son with Lola, he's convinced by Mary to spend time with his son but not to claim him officially. Later at a celebration, he is joined by Narcisse whom requests Nostradamus be killed for misdiagnosing his son with Plague. He orders guards to take Nostradamus away for questioning. After Mary, Catherine, and himself discuss their options to deal with Narcisse, he's told by Mary that she was indeed the one whom ordered Narcisse's son be locked in the a room filled with people who had the Plague.
Later that day, he and Mary take a stroll on the grounds and decide what to do. He gets angry at Mary for having Narcisse's son killed. They decide to look for something to blackmail Narcisse with so that he'll step down. Later that night, he's joined by Bash who tells him that the dead are still among the living due to being murdered. He and his mother go to his father's tomb, they discuss whether he should claim his son or not. Narcisse comes to Francis to convince him that he needs him to keep the country afloat. When Louis joins them Narcisse accuses him of being a protestant. He's assured by Louis that this is not true and that he should trust no one but himself. The next day, he and Mary put on an act to play Narcisse into giving in. He later gives Bash the role of King's deputy. Later that night, he's requested to join Mary in the nursery where she tells him to claim his son. A wet nurse possessed by his father walks in on him with his son calling him a usurper.
In Coronation, Francis and Mary are ushered by his mother whom shows them all the preparations for their coronation. When both he and his wife protest that its in poor taste to throw such a large party when the country is starving. His mother tells them its to show the leaders of other countries that France is not to be messed with. When Mary and Catherine begin to argue Francis' breaks it and tells them his plan to get grain from Lord Ducasse. He then leaves Mary to discuss the grain situation with Lord Ducasse. When on his way back to Mary he's approached by Lola who is unpleased that he dismissed Caroline, one the baby's nannies. When he finds Mary again, Narcisse joins them and they begin to argue about the lack of grain they are receiving from Narcisse. When he leaves, in anger Mary tells Francis to simply take Narcisse's lands and be done with it. Francis knows however that in doing so he would anger all the nobles.
Later that night at a celebration, Lord Ducasse accompanied by his family goes to Francis with his concerns about Narcisse's if he gives his grain. He then goes to Sebastian to find out more about Lola's nanny to know if she was possessed or simply playing a trick. While dancing, he's told by Mary a deal offered by Charles Schuler to supply grain in exchange for having German prisoners released. The next day after he learns that Ducasse has decided not to give away his grain, Francis and Mary again discuss their options on how to handle the famine. He later returns to the Tent City, to go see the man who discusses with ghost to ask if he could tell if Caroline was possessed or not. He brings Caroline in the tent, Henry again takes possession of the woman. He tells Francis that he knows he killed him. Francis warns his father to stay away and returns to his chambers and Mary tells him that she agreed to the deal with Duke Schuler.
The next day, when at a spectacle Duke Schuler returns angry to tell them that the prisoners where not were Mary said they would be. Francis yells for everyone to lower their weapons. He and Mary converse in private about how to deal with the situation. He's later shown by Mary that Condé has returned with the prisoners so that they can salvage their deal with the Germans. He and Mary go to Narcisse to tell him of the new deal for grain, taking away the power he had against them. Later, he and Mary attend their coronation where they are declared King and Queen of France. They retreat to their chambers after and make love.
In The Lamb and the Slaughter, Francis reminisces with his mother about the christenings of his younger siblings as everyone in the castle prepares to celebrate the christening of his son with Lola. He talks about the possibility of his sister who is the Queen Consort of Spain being the godmother of his son and how his mother was denied for the job as well as the idea that Francis doesn't think a big celebration is necessary; however if Francis wants to claim his son publicly then a big party is the way to do it.
Later, Francis and Mary are sharing a moment by the lake and they remember the fun times they had together as children. Mary gives hints and finally confesses to Francis that she is pregnant at long last and that she didn't say anything at first because she wanted to be positive. Francis is ecstatic about this news as he embraces his wife happily. In their chambers, Francis and Mary are under their covers laughing happily about their baby when Catherine bursts into their room ranting with overwhelming happiness about her new unborn grandchild of how she hopes it's a son as there's time for daughters later. She had Mary's chamber pot tested, she's noticed signs that Mary was pregnant for some time though Mary still has her trim figure, and finally one of Catherine's ladies saw Francis and Mary embrace happily by the lake. Mary and Francis are more than a little stunned by how happy Catherine is and Mary says to Francis "Tell me again how happy you are?"
At night, Francis and Mary attend the pre-christening party which is a little slow getting started despite the dancing music, so Francis chats with Mary. The next day, Francis gets to hold his son at the christening ceremony in the castle chapel where the baby is named John Phillip Valois-Angouleme 1st Baron of Vallie.
Later, Francis visits Mary in their chambers after hearing from Conde that she is not well. When Francis arrives he finds his wife in tears as she tells him that she has lost their baby and Mary weeps in Francis' arms as he comforts her. During the night, he takes her to their balcony and shows her a lanterns floating in the sky for her. Francis tells Mary that the world is cruel and unfair and that they will get through it together. 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 questions Francis to what he's been doing. He claims that he's been visiting his son more frequently but she knows that he's been playing dice with Dash. She assures him that she can get pregnant again and that he doesn’t have to be so secretive with her. Later, Francis finds a shard of the lance he used to kill his father on his bed. He soon confronts Caroline and she doesn't understand to why she's at the French Court. He sends to the infirmary to be checked out. Eventually, a group of Catholics burns down a Protestant church and murders Conde’s nephew which causes Francis to punish the Catholics. However, when he sees Caroline, she is once again possessed by the spirit of Henry. No longer being able to take his father's attacks towards him, Francis confesses to his father's murder which Narcisse happens to hear. Francis eventually finds out that the whole thing was all an act. Caroline pretended to be possessed by Henry and was paid for it by Narcisse. Since Francis’ crime is treasonous and grounds for punishment by death, Narcisse leverages his blackmail to free the Catholic prisoners. He also forbids Francis from telling Mary the truth because that would make her an accomplice to treason. After Francis tells Mary he’s changed his mind and decided to free the Catholics, she knows Francis is hiding something. Francis plays on Mary’s insecurities over her failure to bear him an heir and claims he’s disappointed in her and that’s why he’s been distant. Hearing this automatically breaks Mary's heart.
In Three Queens, after Mary decides to join Catherine on a trip to a noble's party, both Queens soon go missing and Francis calls out a search party. Near the end of the episode, Francis and the others finally find Mary and Catherine. When they return to the castle, Catherine tells her son to 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 thousand miles away playing her rule out of duty. Francis quickly tells Mary that he didn't mean what he said back in the previous episode. He promises to fix the space that’s between them.
In The Prince of the Blood, Narcisse pressures Francis into signing an edict which would force all citizens of France to publicly declare their faith in front of the king. Francis gives Mary time to figure something out. He is also reunited with his sister, Claude. Meanwhile, he tells Bash of him killing their father. The two work together to figure out a way to get rid of Narcisse and his minions. Catherine shows Francis an English cipher key she found on the guardsman spy from last week. Francis seeks Lola's help to plant the key at Narcisse’s house to accuse him of treason and put him to death. However, she lets him down when she tells him that she did not hide the cipher in Narcisse’s residence and she demands that he stop using her as a pawn in his political games.
Just in time, Conde and other nobles step forward and present themselves as Protestants. Thanks to them, Francis refuses to sign the edict. However, he finds out that Narcisse has witnesses to Mary and Catherine's part in Henry’s assassination attempts as well. In order to protect his wife and mother, he signs the edict. Mary confronts him and he still refuses to tell her the truth. She states that she is done and he tells her to leave him and France.
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 suggests that she return to Scotland but she refuses. His brother tells him that if he keeps pushing Mary away, he will lose her. Later, Mary and Francis are told by Louis that the minister wants to rebuild the Protestant church. Francis is threatened by the Vatican that he will start a war killing Catholics by setting off explosives planted somewhere in the kingdom if the Inquisition doesn’t stop within two days. Francis has him arrested and sends Bash to find the explosives. When having the pastor tutored, the torturer snaps the pastor's spine on the rack. The Protestants hang the pastor upside down, crucified on a cross in the main square, inciting a riot amongst France’s people. Mary then blames Francis for everything.
In Acts of War, Francis and Mary work together to perform acts of goodwill across the kingdom to smooth over the death and crucifixion of the Protestant minister. She proposes a political marriage between Princess Claude and Louis Conde. The match between a prominent Protestant prince and French Catholic royalty would serve as a gesture of goodwill to the divided kingdom. Francis is against the idea at first but eventually agrees to it as he finds it to be a great advantage towards Narcisse's blackmail. He and Bash create a plan to get him out of Narcisse's influence and kill all of Narcisse’s witnesses against him. Francis pretends that he has lost his mind and is trying to divide the nation. The plan is successful and the brothers leave the castle to get rid of Narcisse's witnesses. Unknown to the two of them, Protestant assassins snuck into the castle to kill Francis and Mary. When Francis returns to the castle, he learns of Mary's rape.
Francis seeks revenge in Mercy. As Francis tries to find Mary's rapists, he decides to tell her the truth about how he was the one who killed Henry and of Narcisse blackmailing him. This strains their relationship even further and later on, Mary manages to kill her rapists with Conde's help. The next day, Mary blames Francis for her rape and tells them that they need to spend some time apart.
Francis tries to repair his marriage with Mary in Getaway.
In Banished, Mary explains to Francis that she saw him asleep with Lola and the baby the previous night when visiting Lola's chambers. Francis tries to explain to Mary that there was nothing going on and that John was sleeping and he didn't want to wake him. However, Mary tells Francis that it was a glimpse of what he could have if he was with Lola instead of her as she has failed to give him an heir. Although still incapable of being touched by him, Mary agrees to help Francis delegate out Narcisse's lands.