In this historical drama, Mary must battle Queen Elizabeth I, her brother James, the Scottish Lords, the Scottish protestants, her husband and herself to secure the crown for her son and heir, the future James I of England.

In 1560 France, the Scottish queen, Mary Stuart, loses her young husband, King Francis II, to a brain infection only a year after their marriage. Resentful and distrustful of Mary, the king's mother, Catherine de Medici, declares herself regent of France until her younger son can assume the throne, leaving Mary powerless. Learning from Scottish messenger James Hepburn, Lord Bothwell, that her mother has died and her half-brother James is now regent of Scotland, Mary agrees to return home to calm her battle-torn country and claim the throne of England where her cousin Elizabeth Tudor has ruled for nearly two years. In England, Elizabeth's close advisor, William Cecil, cautions the queen that the strong French Catholic influence in Scotland is a serious threat to the northern border and will continue to stir the volatile relationship between English Protestants and Catholics. Elizabeth is distracted from events in Scotland when the wife of her lover, Robert Dudley, is found dead. Hoping to quell rumors that Dudley arranged the murder in order to marry Elizabeth, the queen orders Dudley from the court until a trial can exonerate him. In France, Mary is angered upon receiving notice from Elizabeth that she cannot cross through English territory to reach Scotland. Before Mary's departure by sea, Catholic cardinal De Guise presents her to Father Ballard and Italian David Rizzio, both of whom will travel with the Catholic Mary to assist in dealing with the Protestant Scottish lords. Arriving in Scotland, Mary is disappointed by the lack of ceremonial greeting given her by her brother James and the dour lords. Asking after her horses, which were transported by Bothwell's ship, Mary is surprised to hear from James that Bothwell's ship was commandeered by the English and Bothwell imprisoned. Suspecting that James is not pleased by her return and has been instrumental in Bothwell's apprehension, Mary greets the Scottish lords and, hoping to assuage her brother, announces that James will be her chief minister. Riding to Holyrood castle, Mary is disconcerted by the bitter harassment heaped upon her by Reverend John Knox, who scorns Mary's Catholicism. Some weeks later in England, Elizabeth oversees the exercise of Mary's horses and is pleased when Dudley returns to declare he has been cleared of all involvement in his wife's death. Although Elizabeth again refuses to wed the ambitious Dudley, she grows concerned that the impulsive and romantic Scottish queen will re-marry a Catholic, which would be viewed as an act of war against England. Elizabeth conceives of a plan where she will publicly offer to make Mary her successor in the event of Elizabeth's death if Mary will agree to marry Dudley, who has been made the Earl of Leicester. Privately, however, Elizabeth schemes with Cecil to send Bothwell to Scotland, escorted by the handsome, young Henry, Lord Darnley, to convey the offer of succession to Mary. Certain that Mary will scorn Elizabeth's offer and recklessly seek to declare her independence by a romantic entanglement with the English, Catholic Darnley, Elizabeth assures Cecil that in the event Mary should choose to marry Dudley, England will win in any case by placing a Protestant in the Scottish court. Over several weeks Mary becomes involved with Darnley, unaware that the vainglorious young man is secretly also romantically engaged with Rizzio. When Mary announces her intention to marry Darnley, James rejects the plan, declaring that Knox will never approve of a Catholic royal consort. Infuriated by James' continual condescension and refusal to allow her involvement in the country's politics, Mary summarily dismisses him as chief minister, appointing Rizzio in his place. Bothwell warns Mary that she must imprison or execute James to break the Protestant lords' loyalty, but the queen refuses and exiles her brother to England instead. To Bothwell's disappointment, Mary weds Darnley, but Bothwell nevertheless swears his unwavering loyalty and personal dedication to the queen. Although, Mary soon experiences Darnley's willful arrogance and cruelty, she is nevertheless delighted to learn that she is pregnant. After Mary strips her husband of all authority and lavishes attentions on Rizzio, an insanely jealous Darnley accepts an offer made by the head of the Scottish lords, Ruthven, to assassinate Rizzio and overthrow Mary. In London, Elizabeth is provided a copy of Darnley's covenant with the lords and informed by Cecil that everyone in the Scottish court is aware of the plot except Mary and Rizzio. On Cecil's advice, Elizabeth funds James' return to Scotland, hoping to appease the lords. The act is futile, however, as Ruthven leads an incursion to the queen's private rooms where Rizzio is slaughtered as Mary and the vengeful Darnley watch. Fearful that James' return will instigate the lords to go further, Mary and Darnley accept Bothwell's protection at Hermitage Castle. Soon after, Mary gives birth to a son, christened James. Bothwell then leads an army against the Scottish lords who are defeated and exiled after which James imprisoned in Dunbar Castle. Mary agrees to hang James for his betrayal, but he tells her if he dies, she must also execute Darnley for his involvement in Rizzio's murder. Concerned that if she sentences Darnley he will publicly claim the baby was fathered by Rizzio, Mary pardons James. A few months later, when Bothwell tells Mary that Darnley's reckless promiscuity has resulted in his contracting "the pox," the queen is humiliated. Bothwell recommends recalling the exiled Scottish lords who will take Darnley to account for not supporting them as required by the covenant. To Darnley's dismay, Mary pardons the lords and upon their return, Bothwell is drawn into a plot by James to murder the king consort. Lured to his private home in Kirk o' Field, Darnley rests there one evening, while the queen departs to a previously arranged party. The house, whose cellar is full of gunpowder, is set on fire by the lords, but when Darnley escapes just before the explosion, he is brutally assaulted and killed by several lords. In England, Elizabeth is horrified to learn of Darnley's murder and suspects Bothwell, who only a few weeks later marries Mary in a private Protestant ceremony. Shortly after the service, James arrives at Carberry Hill with troops and threatens the couple. Mary pleads with Bothwell not to fight and when James promises Bothwell safe passage to Europe, he accepts. James then demands that Mary abdicate in favor of her son, threatening to publicize letters to Bothwell that reveal Mary's involvement in Darnley's murder. Bothwell vows to return with an army to restore the crown to Mary if she accepts James' offer of safe passage to England after her abdication, and she reluctantly assents. Soon after arriving in England, Mary meets Elizabeth in an isolated glen and asks for her support in restoring her crown. To Mary's fury, Elizabeth declares that when a court has cleared Mary of involvement of Darnley's murder, she will consider her cousin's request, then places her in protective custody. As Mary's confinement stretches over several years, Cecil pleads with Elizabeth to execute her to put an end to the national Protestant and Catholic divide. Increasingly made ill by her dank quarters, Mary continues to hope for a reprieve and is saddened when her son James refuses to correspond with her. Mary also learns with pain that Bothwell has died, insane, in far-off Denmark. Frustrated by Elizabeth's inability to take action against Mary, Cecil works with Lord Francis Walsingham to provide evidence that Mary is involved in a plot to overthrow Elizabeth. Despite the evidence, Elizabeth declares that if Mary asks her pardon she will grant her exile. Elizabeth arranges to meet Mary once again and although Mary readily apologizes directly to her cousin, but demands a public trial. Elizabeth reminds her of the letters tying Mary to Darnley's murder and warns her there is ample evidence of her involvement in the recent plot. Mary boldly accepts her death but reminds Elizabeth that she must live with having ordered the death of her equal. Soon afterward, a despondent Elizabeth signs the execution decree and days later Mary courageously meets her end.