In the third-season opener, Henry VIII takes his third bride, noblewoman Jane Seymour (Annabelle Wallis), in hopes that he will finally have a male heir. Meanwhile, previously loyal subjects in the North take a stand against Henry's anti-Catholic crusade, which includes seizing millions of pounds in monastic wealth; and his new queen champions the cause of returning his estranged daughter, Princess Mary, to court.
Henry sends Charles Brandon (Henry Cavill) to deal with the Catholic uprising; and while confined to bed due to an old jousting injury, the King takes a new mistress, Lady Ursula Misseldon (Charlotte Salt).
Brandon is unsettled by the viciousness and cruelty with which Henry brings an end to the Catholic uprising as the King puts the leaders to death; and, finally, a male heir is born to Henry and his queen, Jane Seymour, who dies shortly after giving birth.
Cromwell sees a number of assassinations strike close to the court, and that they are actually warnings to him; the King meets with a bishop about writing the doctrine of his majesty's Church of England.
With the quest for a new queen underway, a German emissary to the court suggests the King consider the two unmarried sisters of Duke William of Cleves, but Henry shows an inclination to taking a French bride. A number of clerics take exception to the introduction of Henry's "Six Articles of Faith" doctrine; Henry appoints Brandon the King's representative at court on the occasion of Henry's absence.
The King's oppressive measures against the Catholic Church stir grumblings of war with France and Spain; Cromwell prepares arrangements for Henry's fourth marriage, this time to Anne of Cleves (Joss Stone), and Brandon heads to Calais to meet her, only to find that she is plain and unworldly.
In the third-season finale, Henry tires of the unattractive and uninteresting Anne of Cleves (Joss Stone) and takes a mistress, the comely Katherine Howard (Tamzin Merchant), which rekindles his passion. Anne's cousin, a Bavarian prince, arrives at court and sweeps Princess Mary off her feet, but their happiness is short-lived when Henry sends him back to his own country; with his new powers, Brandon accuses Cromwell of being a traitor and has him imprisoned in the Tower of London.