Henry moves swiftly to annul his loveless marriage to Anne of Cleves, and beds a new mistress, 17-year-old Princess Mary falls in love with Duke Philip of Bavaria in spite of their religions, only to be heartbroken when he is sent away from court; Cromwell's fall from favour is sudden and dramatic. The season ends with Cromwell's beheading.

War looms with France and Spain aligning against England with backing from Rome, so Henry agrees to a politically fortuitous marriage with Anne of Cleves, a plain and unsophisticated German aristocrat he has never met.

Matchmaking begins in earnest as Cromwell schemes to secure the Reformation by marrying Henry to a Protestant wife – but the king's marital reputation precedes him; the condition of Henry's wounded leg turns life-threatening.

Henry remains in seclusion while mourning the queen's death, an opportunity that enemies of the crown seize to murder several friends of the court; Cromwell is disturbed when Henry does not resist his new church's similarities to Catholicism. Meanwhile Henry ends his depression by having sex with Ursula one more time before she returns to her hometown.

The leaders of the Pilgrimage of Grace uprising are put to death, but Brandon is haunted by the cruelty and mercilessness of the suppression and his part in it; Henry celebrates the birth of a son but his joy is short-lived as Queen Jane dies within days.

Queen Jane and Lady Mary bring the toddler Lady Elizabeth to court, and Henry reconciles with her at the Christmas holiday. He also makes promises of pardons and redress of grievances to the leaders of the Pilgrimage of Grace, while making plans to bring them to heel for their insurrection, then using a further uprising as an excuse to have Charles Brandon put the leaders to death.

The rebellion now known as the "Pilgrimage of Grace" begins in earnest, with Henry dispatching Brandon to deal with the uprising; bedridden due to the recurrence of his jousting injury, Henry takes a new mistress: Lady Ursula Misseldon.

Days after Anne Boleyn's execution, Henry VIII weds a third time, to shy, demure noblewoman Jane Seymour – a union that he and his advisers pray will result in a male heir; Henry appears to an apparently pleased court, but secretly Thomas Cromwell and Lord Rich worry for their plans for a reformation. Lady Ursula Misseldon arrives at court to wait upon the new queen, and is soon mistress to Sir Francis Bryan. Lady Mary is threatened with death unless she submits to her father's authority and, under guidance from the Spanish ambassador, reluctantly complies. A number of Catholics, once-loyal subjects, rebel in objection to Henry's crusade against Catholicism and the dissolution of the monasteries, shaking Cromwell's new-found confidence, and enraging Henry.