The difficult pursuit of an annulment approved by the Pope begins when Henry meets and falls in love with Anne Boleyn, a charming lady-in-waiting to the Queen. Determined that Anne shouid become his new Queen and provide him with a legitimate son, Henry separates himself from his wife and the Catholic Church. When he fails in his attempts to have a son with Anne and instead has another daughter, Elizabeth, he is quick to lay the blame at Anne's door. He meets Jane Seymour, shy daughter of a knight. Convinced that his future lies with Jane, he takes the chance to be rid of Anne when his friend Charles Brandon tells him of rumors suggesting that she has been unfaithful. Anne is quickly brought to trial, found guilty and executed.

Although Henry's personal life improves with his marriage to Jane Seymour, who helps reunite him with his daughters, his position is threatened when Catholics in the north start to rebel against him. He crushes the rebellion and brutally punishes those involved. Finally his wish comes true when Jane gives birth to a son, Edward, but she falls sick and dies from childbed fever a few days later, leaving him in a deep state of depression. He remains a widower for three years until Thomas Cromwell persuades him into a fourth marriage with the German princess Anne of Cleves. Henry is disgusted by her when he finally meets her. Unable to escape the betrothal, he marries her but starts annulment proceedings soon after.

Henry notices the beautiful Catherine Howard and decides to marry her because she makes him feel young again. She is executed once her hidden past relations with Francis Dereham and her adulterous affair with Thomas Culpeper came to light. Henry later marries his sixth and final wife, Catherine Parr, a wealthy widow closer to his age. She is a loving stepmother to all three of Henry's children and is made Queen Regent during Henry's absence in France. Bishop Gardiner and others suspect her of heresy and nearly have her arrested for it, but she is able to convince Henry of her devotion to him. Henry's health declines until his death in January 1547.

The second season sees Anne reach the peak and end of her power. She is created as Marquess of Pembroke in her own right, and is taken to France to meet King Francis I as the future Queen of England. She sleeps with Henry and conceives a child, whom she is confident will be a boy. Soon afterward, Henry marries Anne and crowns her as Queen, his marriage to Katherine annulled by Archbishop Thomas Cranmer. However, Anne and Henry's hopes are dashed when she gives birth to a daughter, Elizabeth. Anne is ordered by her father to do everything to win back Henry's love, as his lack of attention becomes evident after her miscarriage of her second child and his growing interest in her lady-in-waiting Jane Seymour. Anne encourages Henry to disinherit his elder daughter Mary but tries to establish ties with her on the condition that Mary accept her as queen, but Mary rebuffs this offer. Anne conceives again but experiences another miscarriage, which convinces Henry that his relationship with Anne will never result in male children. Encouraged by Henry and his desire to end his marriage, Anne is eventually accused of witchcraft, incest and adultery. Henry removes Elizabeth from the line of succession, convinced she is not his daughter, and sentences Anne to execution by beheading, which she goes to with dignity, gaining admiration from the people. Anne re-appears in the final episode of Season 4 in the dream sequence alongside Elizabeth, expressing pride for her clever daughter, proclaiming her innocence that the crimes she was killed for, and showing sympathy for her deceased cousin Catherine Howard.

Because of Katherine's seeming inability to have living sons, along with the onset of the menopause, Henry worries that England might face a reversion to civil war in the event of his death. With the Wars of the Roses still a recent memory, he is determined to have a legitimate son to inherit the throne. He therefore prefers to believe that Katherine lied when she swore that her previous marriage was never consummated and that therefore his marriage to her is incestuous and invalid. She is banished to spend her final days at the manor "The More", without any contact from her daughter Mary. However, Henry is shown to genuinely care for Katherine, as shown when he tearfully informs her of his intent to divorce her. She is last seen dictating her will on her deathbed, intercut with it read aloud by a mournful Henry; Anne Boleyn smiles upon hearing the news and states that "Now, I am indeed queen." Katherine re-appears in the final episode of Season 4 in the dream sequence alongside Mary, confronting Henry about his mistreatment towards their daughter and her own status as his 'true wife'.

In the second season, Cromwell rises to the position of Lord Chancellor after the fall of More (in actuality he was never Lord Chancellor although the chief minister). Cromwell is depicted as being ruthless and calculating, but also as a hard-working and extremely capable minister; he is Wolsey's successor as the King's right-hand man. His role as a talented administrator and reformer eventually comes into conflict with Henry's ambiguous commitment to the Reformation. Cromwell orders swift and necessary action when allegations arise regarding Queen Anne Boleyn (which leads to her ultimate downfall) at Henry's orders, but sees the Reformation slipping away, with the Church of England, despite its break from Rome, retaining Catholic tradition and ritual. An attempt to strengthen the King's ties to Protestantism through a marriage to Anne of Cleves (though couched as a political alliance) backfires. Because of his common origins, he is resented by nobles and frequently abused even by Henry. Cromwell's beheading is a botched affair because the executioner is drunk.

He is deeply loyal to Anne Boleyn but, despite his devotion to her, he is forced to relinquish their mutual desire for a reformed faith when Anne falls from favour. He takes her last confession in the Tower and breaks the news to her that Elizabeth is to be declared illegitimate, but promises her that he will endeavour to keep her in the King's "good and kind graces". Historically Cranmer lived until Henry's daughter Mary inherited the throne, when she, a Catholic, had him burnt at the stake for his Protestant beliefs.

Chapuys has the distinction of being the only character to feature prominently in all four seasons without ever being a starring cast member. His origin and ultimate fate were changed for the series: historically, he was a Savoyard rather than a Spaniard as suggested in the series, and he retired to the Low Countries, where he set up a small college in 1548. He died in 1556, meaning that he lived into Mary's reign.

Despite her unhappy marriage and the scandal of her in-laws, Jane is asked back to court by Queen Jane and is appointed as her principal lady-in-waiting. Jane secretly helps the Queen to get funds to the Lady Elizabeth's governess when Henry refuses to pay, and arranges the public return of Lady Mary to court. Lady Rochford is a keen supporter of the Reformation and abhors the Catholic faith, although she is so moved by Jane's actions that she puts aside her opinions. She is later seen as a lady-in-waiting to Queen Catherine Howard, whom she despises, but facilitates the Queen's clandestine affair with Thomas Culpepper, who is obsessed with Catherine. Once the affair comes to light, she is interrogated and arrested for treason and has a nervous breakdown. Despite Lady Rochford being declared legally insane, King Henry VIII has a law enacted to make it legal to execute her by beheading. She is executed on the same day as Queen Catherine.

In the aftermath of Anne's execution, Henry is initially unwilling to have anything to do with Elizabeth, claiming not to believe that she is his child, but when Elizabeth's half-sister, Mary, and stepmother, Jane Seymour, arrange for her to be brought to court and presented to her father for Christmas 1536, she is welcomed. She later attends the christening of her half-brother, Edward, and goes to live at Hundson with Mary. In 1540 Elizabeth and Mary are present at court to greet their newest stepmother, Anne of Cleves. During Henry's marriage to Catherine Howard, Elizabeth is much warmer to her than Mary, but makes no secret of her preference for Anne of Cleves, and spends most of her free time at Hever Castle (Anne's residence and Elizabeth's ancestral home). Elizabeth treats her restoration to the succession with dread, and declares to Mary, with God as her witness, that she will never marry.

Elizabeth develops a closeness to her sister and brother. She is seen to be good friends with Anne of Cleves and, in the fourth season, grows close to Catherine Parr, who vows to raise Elizabeth in the faith of her mother. However, throughout all of this, she and her father remain somewhat distant. By the end Henry acknowledges, while conversing with the spirit of Anne Boleyn, that he has always been proud of his daughter and does recognise that she is very intelligent. He also reveals that he wishes that he could have shown her more affection but that her resemblance to her mother (Elizabeth looked like her father, but had her mother's eyes and personality) made him keep her at arm's length.