The relationship between half brothers, Francis and Sebastian. They grew up together always had each other’s backs, but there was also a lot of underlying tension between them. And when Mary showed up, it caused tension between the brothers.
Their relationship had been completely broken due to Bash lying to Francis several times, hiding things from him, and his feelings for Mary. In Francis' eyes, Bash had betrayed him. It had became even more strained when Francis returned to the French Court and Mary chose Francis over Bash. Bash was exiled, never to return to France. When Bash learned of the Darkness, he returned to the French Court to get help so that he could save Rowan and get rid of the creature before it could hurt anyone else. Francis agreed to help Bash and was caught up in a life and death situation until Bash saved him. They finally were able to work things out, repairing their relationship.
During the events of the second season, Bash became the King's Deputy as a request from Francis.
In the Pilot, Francis is travelling through the castle and comes across his father’s bastard son, Sebastian. They joke about Francis’ promiscuous activities before Sebastian sends Francis to his parents, who are preparing for his sister, Elizabeth’s, upcoming wedding to a Spanish royal.
In Snakes in the Garden, Francis finds Bash in the woods and his brother insists on bringing Colin back to the castle, as Mary would like her subject to have a proper burial. It's not the guards that got to him like Francis thought, though, since they hang traitors up by the necks and not their feet. Bash concludes that it's the vagrants who are living in the woods that cut Colin's throat and cuts his own hand to ward off the shadows that suddenly enveloped him and his brother. Following a quick saying in another language and the blood being spread around, the boys are safe and load Colin's body onto a horse before riding back.
Francis confronts Bash about going out into the woods on Mary's command and the latter mentions that he feels as if its his duty to protect her, though Francis doesn't believe that was the reason for a second. And from now on that Bash never lie to Francis again.
In Kissed, Francis interrupts Bash and Henry sparring, once again asking for men to send to Scotland. Francis tells Henry his reasoning why, but Henry turns him down anyway. Francis offers to spar with him, saying if he wins they will send men and if he loses he won’t mention it again. Henry doesn’t think it is a good idea but they end up sparring. Francis wins but Henry refuses to send troops. Bash tries to give Francis advice but he doesn't want it.
At the party that evening, Mary and Francis dance, arguing about the need of France to assist Scotland. Francis says he has done all he can, but Mary thinks he can do more. Tomas cuts in without asking, telling Mary he had the musicians play music from his country. Francis stands off to the side with Sebastian to watch, as Thomas pretty much makes his intentions to clear. Sebastian teases Francis, asking why he doesn’t dance like that and Francis tells him to shut up.
Francis, once again, confronts his father and tells him that they need to send troops to Scotland. He calls out the inappropriate relationship that must be going on between Kenna and Henry, and threatens to inform Catherine and Diane, knowing it would make Henry’s life difficult. Henry relents, saying they will send men, but win or lose Francis will have to answer for the outcome. Henry tells Francis to send France’s fastest rider to the companies of men to mobilize them. Sebastian, dunking his head into water to sober himself, is apparently the fastest and Francis gives the command to send him to the troops. Francis is worried about Sebastian’s condition, but Sebastian says he can do it and rides off.
In Hearts and Minds, Francis and Bash team up in this episode. Francis is speaking with Sebastian, trying to figure out why the English would attack French troops since they are not at war with each other. Catherine comes in and accuses him of thinking too much with his heart. Francis tells her that he doesn’t trust Thomas, and he is afraid that Mary is going from one waiting king to another. When Francis begins asking questions about Tomas, Francis tells Bash there have been rumors that Tomas murdered his first wife. Francis wants to somehow prove this before he leaves with Mary. Tomas interrupts them and tells Francis that Mary is now his property, and anything that happens to her is none of Francis’ concern. Before Francis can attack Tomas, Bash stops him. After Tomas leaves, Sebastian says that Thomas is a monster and that if Francis won’t kill him, Sebastian will.
The next day, Francis joins Bash and Lola and the three discuss Tomas and his change in his personality. Tomas had been searching the continent for a queen, because he would not have been declared legitimate otherwise. They realize that Mary would not have needed Tomas and his men if the French was not ambushed, and realizes that it must have been Tomas as the spy. Francis, Sebastian and some guards approach Tomas and Mary, and Francis explains his theory of what actually happened. Mary catches on quickly and Tomas storms off, saying they would need proof if what they think is actually true. Mary thinks Miguel will help them, since he hates Tomas. She also thinks they should get the prostitute that accused Simon because she was probably forced as well. She tells Francis they need to get proof before Simon is killed, because then England will be at war with both France and Scotland.
Lola meets Francis and Sebastian on the lawns, informing them that a servant saw Miguel following Thomas on the game trails. They realize that Thomas will try to kill Miguel and make it look like a hunting accident, so no one will be able to get the truth out of Miguel. Francis and Sebastian stop Thomas from killing Miguel, but Thomas does hit Miguel with an arrow in the back.
While Francis checks on Miguel, Sebastian holds a sword to Tomas. When Sebastian is distracted, Tomas pulls his own sword and starts fighting with Sebastian. In his weakened state, Tomas gets the upperhand and Sebastian is pushed down. Francis starts sword fighting with Tomas, and tells Francis that he doesn’t know how to take like a bastard does. Eventually, Francis is pushed down and Tomas attempts to shoot him with an arrow. Sebastian pulls a dagger and throws it at Tomas’ leg, causing him to miss his shot. Francis puts a dagger to Tomas’ chest, pushing it through when Tomas tries to pull the dagger in his leg out to attack Francis.
Francis goes to help Sebastian, whose wound has opened and he is bleeding through his shirt. Sebastian can see that Francis’ hands are shaking, and tells Francis that killing isn’t supposed to be easy and the fact that his hands are shaking makes him different than Tomas.
In Chosen, Francis is still fuming because he saw Mary kissing Sebastian, and he gives her the cold shoulder. Mary discusses the kiss with Sebastian, and the two of them are still clueless that Francis knows about it. Bash speaks to Francis and Mary about the situation he's put himself in including how Mary has been chosen to be the next sacrifice. Francis is even more angered with his brother and tells him how there are too many secrets between them, referring to how Bash knows so much about pagans as much as his kiss with Mary.
The next day, a stag's head is hanging above Mary's bed while she is sleeping. She isn’t in great shape when the stag’s head is taken down. Bash comes in to check on her and Francis, who is already there, pulls him right out of the room. The stag incident has him eager for Bash to deal with the pagan problem. When Bash reminds him about exactly what dealing with the problem entails – rather gruesome murder – Francis neither pushes nor backs off. He’d clearly like Bash to find another way, but he still blames him for Mary becoming involved.
By the end of the episode, Francis launches into a lecture about how Mary and Bash’ actions put them both in danger, both from the pagans and potentially from himself. Not that he wants to hurt anyone, but jealousy can warp a person’s mind. He doesn’t seem proud of it, but he admits that there were times when he thought that if Bash died while trying to pay his debt he’d have deserved it. One day Francis will be king and there could be nasty consequences to his darker moods. One day he hopes they will be married, but it won’t happen if it’s not right for France and Mary needs to be open to better situations for Scotland to. They are rulers and they can’t let things like love triangles cloud their judgment. Until they can be sure they’re getting married he’s going to keep his distance, which means he has to accept that she can spend her time with other people. Mary translates this as her having to accept that he can spend his time with other people, mainly Olivia. Francis doesn’t deny that, but says it does go both ways. Mary can be with anyone she likes. So long as it’s not his brother. Before Francis leaves, Bash asks him if that’s a warning. Francis says it is.
In For King and Country, Francis goes to the dungeon and fights Bash. Bash either won’t or can’t fight back. Mary arrives and puts a stop to it, informing Francis that Bash only knew about the prophecy regarding Francis’ death and this new plan, where Bash is her husband and the king of France, is all her idea. Bash’s obvious surprise – and not happy surprise – backs her up. Francis lists off everything that he, his mother, and his brothers who aren’t Bash will lose because of this and says he won’t forgive Mary and Bash just because they think they’re protecting him.
Francis tells Bash that their reversal of fortunes is ironic and says he plans to enjoy the freedom that used to be his brother's then leaves the French Court.
In Royal Blood, Mary believes that Bash wants the Charles and Henry Jr. to leave the French Court is because they remind him of Francis.
Bash and Francis are reunited in Consummation. They get into a fight over who gets to marry Mary. Near the end of the episode, Mary chooses Francis and Bash is exiled from the French Court. The guards escorting Bash to the ship that will take him to Spain, try to kill Bash and he believes that his brother tried to have him killed.