Henry succeeds in having himself declared "Supreme Head of the Church and Clergy in England," but with a caveat; Pope Paul III (Peter O'Toole) has his own idea about how to deal with the "Great Matter" of the king's annulment; Henry selects an obscure cleric (Hans Matheson) to be his personal chaplain; an attempt is made on the life of Bishop Fisher (Bosco Hogan); Henry issues a command to Queen Katherine.
Henry engages in more attempts to undermine the Catholic Church's power in England, and sends his personal chaplain (Hans Matheson) to Germany to learn more about the Lutherans; Anne decides it is time for her and the king to consummate their relationship; Charles Brandon begins to sow seeds of doubt regarding Anne's virtue.
Henry finally runs out of patience and weds a pregnant Anne in a secret ceremony; Cromwell is appointed chancellor after Thomas More steps down; the Pope condemns Henry's behavior and threatens him with excommunication; Katherine is warned not to return to court; an assassin targets Anne.
Henry commands his people to swear an oath of "allegiance and recognition of the King's supremacy" to both church and state, an oath Sir Thomas More is not wont to accept; the King's womanizing ways are brought to the attention of Anne, who arranges, and gives her blessing to, his next mistress. Also, Anne has a confrontation with Henry's daughter, Lady Mary.
Bishop Fisher and Sir Thomas More are charged with high treason and imprisoned for refusing to sign the oath of allegiance; complications arise with Anne's pregnancy; Henry's lust leads him to once again cheat on Anne; Thomas Boleyn enjoins his daughter Anne "not to lose the king's love," while Mary Boleyn returns to court with a pair of surprises.
Sir Thomas Cromwell garners more power as Henry's right-hand man; Anne's insecurity and her concerns about her place in court intensify; Henry is haunted by memories of Sir Thomas More's execution; the king continues to cheat on the queen, who broaches the idea of betrothing their daughter, Elizabeth, to a French royal and gets a most insulting response.
The Reformation is in full swing and the Catholic Church loses power; Anne Boleyn fears her own powerful position as queen is in danger from the perceived threat of Queen Katherine and Mary, the daughter of Henry and Katherine; Henry receives some unfortunate news.
Henry is smitten with Jane Seymour (Anita Briem) and appoints her a lady-in-waiting to Anne, who is none too pleased; Henry is dealt a serious injury while jousting, leading to speculation about who would be his successor.
The fortunes of Anne and her family plummet at court and with the King when she loses a son; Henry's affections seem to have switched to Jane Seymour, as he awards her family a place at court; palace intrigue intensifies as members of court make a move against Anne, who is accused of adultery.
In the second-season finale, Anne and her alleged adulterous lovers are sentenced to death. Henry declares their marriage to be null and void, meaning daughter Elizabeth is considered illegitimate and is no longer a successor to the throne. Henry then asks Jane Seymour to be his next queen in hopes of siring a legitimate male heir.