Together they have to balance their marriage with their roles as monarchs, and deal with the rising religious conflict between Catholics and Protestants, as well as the ambitions of the rival House of Bourbon for the throne of France.
Mary and Catherine clash when powerful noble Eduard Narcisse (Kjartan Hewitt) demands they throw his rival Pierre Voland in with the sick.
Eduard's father, Stéphane Narcisse (Craig Parker), arrives to investigate his son's death, and arrests Nostradamus to take the fall for Mary's decision.
While King Francis is busy, Queen Mary makes a deal with Herr Schuler (David Jansen), a German duke, who offers grain in return for the release of Protestant prisoners.
The revelation is that Caroline has been in the pay of Lord Narcisse; that she had fabricated being possessed by Henry II of France's spiritual essence in order to get the King into confessing to his father's murder.
Lord Narcisse hears this confession and blackmails King Francis into letting the Catholic murderers of Emile go free.
They encounter a pair of actors, Roger (Ari Millen) and Jenny (Charlotte Hegele), who are pretending to be the King Francis and Queen Mary.
Lord Narcisse demands that King Francis sign an edict that will force everyone in France to openly declare their religion.
Lady Lola is tasked by King Francis to plant false evidence that would get Narcisse arrested as a traitor but she claims she was unable to go through with it.
As a result of Francis' Edict of Romorantin, Cardinal Vasari (Salvatore Antonio) from Rome is torturing suspected Protestants.
Queen Catherine tries to send her surviving daughter away by marrying her off to the son of a Bavarian count, but the Princess sabotages this by making public sexual overtures on Lord Narcisse.
Queen Mary suggests that Princess Claude, who is Catholic, and Prince Louis, who has converted to Protestantism, be wed as a symbol of interfaith relations.
While King Francis and Bash are away in an attempt to destroy Sir Montgomery, a group of Protestant assassins sneak into the castle.
King Francis and Queen Mary learn that King Antoine is thinking of allying with their enemy, Queen Elizabeth of England as he believes that Bash had killed his and Prince Louis's elder brother, Prince Marcus, during the Italian Wars, and wants vengeance, either by killing Bash or seducing Lady Kenna.
When Queen Mary turns down another of King Francis's attempts to reconcile, he has sex with Narcisse's niece, Amelie (Siobhan Williams).
King Francis, as advised by Lady Lola, tells Queen Mary that she can be with Prince Louis as long as she is discreet.
Protestant radicals take a monastery hostage in retaliation for Francis's sending troops to Scotland, but Bash and Renaude recover it successfully.
Louis fears he's no longer safe in France, so when he's approached by another English envoy, Lord Akers (Vincent Gale), he accepts Elizabeth's proposal.
Louis immediately takes part in a secret proxy wedding, making him King consort of England and a traitor to France.
Akers returns to rescue Prince Louis, informing him that Elizabeth still wishes to marry him, and wants him to take the crown of France for her.