In August 1561, a 19-year old woman steps onto land from the deck of a splendid galleon. Mary Stuart, the new Queen of Scotland and a Catholic, enters a kingdom divided by squabbles between its nobles and religious strife, including a rising Protestant movement. Queen Elizabeth I, the unmarried head of the Anglican Church, implores her to renounce her claim to the British throne.
Queen Mary has now begun to look for a husband and negotiations are opened for a match with Don Carlos, Son of King Philip II of Spain. Queen Elizabeth makes it clear that such a marriage would be a hostile act. Mary comes to focus her attention on her cousin, Henry Stuart, or Lord Darnley. Because he too is Catholic, tensions mount with Scottish Protestants.
Mary's marriage to Lord Darnley is on the rocks. He is becoming increasingly drunk, angry, and violent. Meanwhile, her pregnancy and the birth of her son James have thrown the fate of England and Europe into turmoil. King Philip II worries about the rise of Protestants in Spain and subjects them to the force of the Spanish Inquisition.
King Philip II expands his war on Protestantism. A soothsayer tells Elizabeth to expect violence and bloodshed in Scotland. Meanwhile, a band of intruders murders Lord Darnley. Mary's lover, James Hepburn, Earl of Bothwell, is tried and acquitted. But as the two marry, Mary's brother arrives in Scotland with an invading army financed by Elizabeth.
The daggers are out for Mary. Her army has disserted her. The invaders present her with a proposal crafted by Elizabeth: dissolve her union with Bothwell. While he flees into exile, Mary tries to gain time. But the negotiations do not go the way she expects. As Elizabeth finds herself under pressure from Spain, Mary and her supporters make a daring move.
Mary Stuart's son James, raised as a Protestant, now rises to the throne of Scotland. With the forces of Catholicism gathering around England, Elizabeth must now deal with her cousin and rival once and for all. Mary's fate, now sealed, would echo down through the history Scotland, England, and Europe. Warning: the ending contains graphic violence.