Elizabeth remains a threat in her childless Catholic sister's eyes. Queen Mary is still on the throne and with her harsh politics, she excessively pursues the persecution of Protestants, even of her sister. Queen Mary knows that her sister has a large number of supporters in England, and therefore, she imprisons Elizabeth in the tower and later puts her under house arrest. When Queen Mary surprisingly dies from a tumor, Elizabeth becomes Queen of England. William Cecil, her advisor, warns Elizabeth of the dangers that the married Robert Dudley may, due to their inappropriate relation, cause as a member of the Privy Council.

The pressure on Elizabeth grows as there is still no marriage and consequently no heir to the throne. Elizabeth fears that her cousin Mary Queen of Scots, recently widowed, might claim her right to the throne of England. However she is resolute in thinking that she can rule alone. Meanwhile she continues to meet Robert Dudley. When his wife dies, rumors spread that Elizabeth might be behind her death. Details of a plot to replace Elizabeth with Mary are uncovered by Walsingham. Even the Duke of Norfolk seems to be involved and is subsequently sent to the tower.

In order to neutralize the threat from the Catholics, Elizabeth pursues a match with the Duke of Anjou. Walsingham discovers proof of a planed murder of Elizabeth. Elizabeth sends the Duke of Anjou away when she finds a knife in her bed and brings Mary Queen of Scots to trial. She is forced to execute her when Mary Queen of Scots is found guilty. This execution angers the Spanish and they send their Armada to fight the English as a consequence. However, the English can defeat the Armada. The news of Dudley's death leaves Elizabeth heartbroken, but when she meets the step-son of Dudley, the Earl of Essex, she allows herself to be charmed by him.