Elizabeth initially did not want to face the heated conflict between Catholics and Protestants in England. But Mary Stuart forced her to do so. The Catholic Mary, queen of Scotland, was the grandniece of Henry VII and next in line to the throne. In the eyes of Catholics, Elizabeth was illegitimate and had no right to the throne. To them, Mary was the rightful Queen of England. Plots were made to make Mary queen and these would have been formed regardless of whether Elizabeth had a child or not. This is perhaps especially so when Mary was Elizabeth's prisoner following her disastrous reign in Scotland.
Accused of murdering her second husband, Henry Stewart Darnley, Mary fled to England to escape a rebellion in Scotland, seeking Elizabeth's help in restoring her to her kingdom. She was immediately imprisoned. This was as much to protect her as to minimise the danger she posed to Elizabeth. Mary was kept a prisoner for almost twenty years. In that time, Elizabeth refused to hear about executing her cousin, but Mary's complicity in the Babington plot of 1586 made the execution, in the eyes of many, unavoidable.
Meanwhile, Elizabeth's throne was threatened from outside forces. Philip II, who became ruler of Spain and its empire in 1556, sought to control the world. England and many other European countries were jealous of Spain's riches, especially in the New World. Elizabeth allowed her seamen to raid Spanish ships on the high seas. Between 1577 and 1580, Francis Drake sailed around the world, becoming the first man after Ferdinand Magellan to do so. On his trip, he ravaged Spanish settlements in South America, returning to England with £1,000,000 in treasure. Elizabeth knighted him aboard his ship, the Golden Hind, worsening already tense relations between Protestant England and Catholic Spain.
During the 1580s, Elizabeth began to harshly persecute Catholics in England. She sent hundreds to their deaths. Many felt the horrors of the wrack, the manacles, and the Scavenger's Daughter. This last device was an iron hoop that brought a victim's hands, head, and feet together into a tight ball until he or she was crushed. Part of the reason for this persecution was a series of Catholic plots to murder Elizabeth and replace her with Mary, Queen of Scots. Finally, in 1586, Mary's part in these plots was proven. She was beheaded the following February.
Mary's death was the final blow to English-Spanish relations. Philip II declared war. In July 1588, a huge navy fleet — the Spanish Armada — set sail for England. The English navy, led by Francis Drake and Martin Frobisher, rose to meet the armada in a nine-day battle. The smaller, quicker English ships easily outmaneuvered the Spanish galleons, but could not come close enough to attack. The Spaniards, however, made the mistake one night of anchoring their entire fleet, and the English sent a squadron of flaming ships into the anchored vessels. Frightened, the armada cut its lines and fled into open water. Chased by the English, the Spaniards tried to sail north around the British Isles. But storm after storm pounded the armada and nearly half the fleet was lost. The war continued for 15 years, but the Spaniards could not overcome the English. When Elizabeth died in 1603, Philip's dream of making England into a Catholic province ended.