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 Stuart decides to marry Lord Darnley. Like Mary, he is a grandchild of Queen Margaret Tudor and has his own claim on the English throne. Mary's relationship with Elizabeth dissolves into suspicion and hatred. The marriage takes place and Mary becomes pregnant. Having an heir would give her an even stronger claim to the English throne.
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.
Philip II heads to England to meet with Elizabeth I. Upon arrival, his complex relationship with Elizabeth and with England begins to unfold. From exile, Mary and her allies plot her return to the throne of Scotland. The armies of the new Protestant leadership head them off. In desperation, she turns to her cousin, the Queen of England.
Mary is now a prisoner in an English castle. A number of allies attempt to intercede on her behalf. King Philip sees her fate in terms of his own global ambitions. Catholics in England see her redemption as their chance to vie for power. Treachery and betrayal abound. After 10 years of captivity, she receives a visitor, her cousin Elizabeth.
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.