At the end of 1562, Elizabeth fell ill with
smallpox, but later recovered. Alarmed by the Queen's near-fatal illness, Parliament asked in 1563 that she marry or nominate an heir to prevent
civil war upon her death. She refused to do either, and in April, she
prorogued Parliament. Parliament did not reconvene until Elizabeth needed its assent to raise taxes in 1566. The
House of Commons threatened to withhold funds until the Queen agreed to provide for the succession. On
October 19, 1566, Sir Robert Bell boldly pursued Elizabeth for the royal answer despite her command to desist; in her own words "Mr. Bell with his complices must needs prefer their speeches to the upper house to have you my lords, consent with them, whereby you were seduced, and of simplicity did assent unto it."
Different lines of succession were considered during Elizabeth's reign. One possible line was that of
Margaret Tudor, Henry VIII's elder sister, which led to Mary I, Queen of Scots. The alternative line descended from Henry VIII's younger sister,
Mary Tudor, Duchess of Suffolk; the heir in this line would be the Lady Catherine Grey, Lady Jane Grey's sister. An even more distant possible successor was
Henry Hastings, 3rd Earl of Huntingdon, who could claim descent only from
Edward III, who reigned during the fourteenth century. Each possible heir had his or her disadvantages: Mary I was a Roman Catholic, Lady Catherine Grey had married without the Queen's consent and the
Puritan Lord Huntingdon was unwilling to accept the Crown.
Mary, Queen of Scots, had to suffer her own troubles in Scotland. Elizabeth had suggested that if she married the Protestant
Robert Dudley, 1st Earl of Leicester, then Elizabeth would "proceed to the inquisition of her right and title to be our next cousin and heir." Mary chose her own course, and in 1565 married a Roman Catholic, who also had a claim to the English throne,
Henry Stuart, Lord Darnley. Lord Darnley was murdered in 1567 after the couple had become estranged. Darnley was a heavy drinker and had approved the murder of Mary's secretary,
David Rizzio, with whom he suspected her of having an affair. Mary then married
James Hepburn, 4th Earl of Bothwell, who was widely believed to be responsible for Darnley's murder. Scottish nobles then rebelled, imprisoning Mary and forcing her to abdicate in favour of her infant son, who consequently became James VI of Scotland.
In 1568, the last viable English heir to the throne, Catherine Grey, died. She had left two sons, but they were deemed illegitimate, owing to the absence of any living witnesses to the marriage, or to any clergy who could attest to having performed it. Her heiress was her sister, the
Lady Mary Grey, a hunchbacked dwarf. Elizabeth was once again forced to consider a Scottish successor, from the line of her father's sister, Margaret Tudor, Queen of Scots. Mary I, however, was unpopular in Scotland, where she had been imprisoned. She later escaped from her prison and fled to England, where she was captured by English forces. Elizabeth was faced with a conundrum: sending her back to the Scottish nobles was deemed too cruel; sending her to France would put a powerful pawn in the hands of the French king; forcibly restoring her to the Scottish throne may have been seen as an heroic gesture, but would cause too much conflict with the Scots; and imprisoning her in England would allow her to participate in plots against the Queen. Elizabeth chose the last option: Mary was kept confined for eighteen years, much of it in
Sheffield Castle and
Sheffield Manor in the custody of
George Talbot, 6th Earl of Shrewsbury, and his redoubtable wife
Bess of Hardwick. Mary was later removed to
Tutbury Castle.
In 1569, Elizabeth faced a major uprising, known as the
Northern Rebellion, instigated by
Thomas Howard, 4th Duke of Norfolk, Charles Neville, 6th Earl of Westmorland and
Thomas Percy, 7th Earl of Northumberland. Pope Pius V aided the Roman Catholic Rebellion by excommunicating Elizabeth and declaring her deposed in a
papal bull. The Bull of Deposition,
Regnans in Excelsis, was only issued in 1570, arriving after the Rebellion had been put down. After the Bull of Deposition was issued, however, Elizabeth chose not to continue her policy of religious tolerance. She instead began the persecution of her religious enemies, giving impetus to various conspiracies to remove her from the throne. She also permitted the Church of England to take a more explicitly
Anglican line by allowing Parliament to pass the
Thirty-Nine Articles. These were not intended as a complete statement of the
Christian faith, but of the position of the Church of England
vis-a-vis the Roman Catholic Church and dissident
Protestants.
Elizabeth then found a new enemy in her former brother-in-law, Philip II, King of Spain. After Philip had launched a surprise attack on the English privateers Sir Francis Drake and
John Hawkins in 1568, Elizabeth assented to the detention of a Spanish treasure ship in 1569. Philip was already involved in putting down a rebellion in the
Spanish Netherlands, and could not afford to declare war on England.
Philip II participated in some conspiracies to remove Elizabeth, albeit reluctantly. The 4th Duke of Norfolk was also involved in the first of these plots, the
Ridolfi Plot of 1571. After the Roman Catholic Ridolfi Plot was discovered (much to Elizabeth's shock) and foiled, the Duke of Norfolk was executed and Mary lost the little liberty she had remaining. Spain, which had been friendly to England since Philip's marriage to Elizabeth's predecessor, ceased to be on cordial terms.
In 1571, Sir William Cecil was created
Baron Burghley. He had been Elizabeth's chief advisor from the earliest days, and he remained so until his death in 1598. In 1572, Burghley was raised to the powerful position of
Lord High Treasurer; his post as Secretary of State was taken up by the head of Elizabeth's spy network, Sir Francis Walsingham.
Also in 1572, Elizabeth made an alliance with
France. The
St Bartholomew's Day Massacre, in which thousands of French Protestants (Huguenots) were killed, strained the alliance but did not break it. Elizabeth even began marriage negotiations with
Henry, Duke of Anjou (later King Henry III of France and of Poland), and afterwards with his younger brother
François, Duke of Anjou and Alençon. During the latter's visit in 1581, it is said that Elizabeth "drew off a ring from her finger and put it upon the Duke of Anjou's upon certain conditions betwixt them two". The Spanish Ambassador reported that she actually declared that the Duke of Anjou would be her husband. However, Anjou, who was reportedly scarred and hunch-backed, returned to France and died in 1584 before he could be married. After his departure, Elizabeth wrote a poem, "
On Monsieur’s Departure", which appears to refer to their failed negotiations; however, the poem is largely a collection of Petrarchan commonplaces and thus not a clear picture of the Queen's private thoughts.