Once displaced by her sister as heir to the throne and then forced to serve as her lady in waiting, Queen Mary certainly got her revenge when she threw Lady Elizabeth into the infamous Tower of London on March 18, 1554.
A woodcut by A. Bouvier of Elizabeth held prisoner in the Tower of London during Mary I's reign.
Queen Mary had just quelled the second Protestant rebellion in her very short reign. The first had put Lady Jane Grey in the tower and ended in the execution of the Duke of Somerset (who had tried to prop up Lady Jane as the legitimate queen of England). And although the Duke lost his head, Mary had been lenient with the conspirators involved in the ill-fated Lady Jane monarchy––most had been pardoned and even Jane had been spared her life. But after Wyatt's Rebellion, in which Jane once again was the focus of a Protestant plot to overthrow Queen Mary's rule, Jane was sent to the executioner's block--not because she took part in the conspiracy but because she was the focus of it. It was clear that as long as the Protestants had a legitimate alternative to Mary's Catholic rule, they would keep trying to overthrow her.
This is what landed Elizabeth in jail. Jane had been the actual focus of the plot, so it was easier to order her execution (in fact, Mary's Spanish relatives insisted it happen as a preliminary to Mary's marriage with King Philip of Spain). But Elizabeth was more difficult. For one she was Mary's sister; She was also a daughter to King Henry VIII and named in his Act of Succession. Plus, Mary could not prove Elizabeth's guilt in the conspiracy. No consipirator had named her as the next queen, and no evidence could be found that she had known of or participated in the plot to overthrow her sister. But with Jane gone, Elizabeth was the next logical focus of Protestant rebels, and it was easiest to just lock her up.
Elizabeth was eventually removed from the Tower, but remained under house arrest in the country until her brother-in-law, Philip of Spain, arranged for her release, her reconciliation with Mary and even for her return to court. Click here to read more about Mary and the Protestant plots to overthrow her.