The tense religious and political climate following the Scottish Reformation that Mary encountered on her return to Scotland was further agitated by prominent Scots such as John Knox, who openly questioned whether her subjects had a duty to obey her.

She issued a proclamation accepting the religious settlement in Scotland as she had found it upon her return, retained advisers such as James Stewart, Earl of Moray (her illegitimate half-brother), and William Maitland of Lethington, and governed as the Catholic monarch of a Protestant kingdom.

James Hepburn, 4th Earl of Bothwell, was generally believed to have orchestrated Darnley's death, but he was acquitted of the charge in April 1567 and in the following month he married Mary.

On 14 December, six days after her birth, she became Queen of Scotland when her father died, perhaps from the effects of a nervous collapse following the Battle of Solway Moss[7] or from drinking contaminated water while on campaign.

[11] Rumours spread that she was weak and frail,[12] but an English diplomat, Ralph Sadler, saw the infant at Linlithgow Palace in March 1543, unwrapped by her nurse Jean Sinclair, and wrote, "it is as goodly a child as I have seen of her age, and as like to live.

[18] Cardinal Beaton rose to power again and began to push a pro-Catholic pro-French agenda, angering Henry, who wanted to break the Scottish alliance with France.

[27] In May 1546, Beaton was murdered by Protestant lairds,[28] and on 10 September 1547, nine months after the death of Henry VIII, the Scots suffered a heavy defeat at the Battle of Pinkie.

The French fleet sent by Henry II, commanded by Nicolas de Villegagnon, sailed with Mary from Dumbarton on 7 August 1548 and arrived a week or more later at Roscoff or Saint-Pol-de-Léon in Brittany.

[37] Mary learned to play lute and virginals, was competent in prose, poetry, horsemanship, falconry, and needlework, and was taught French, Italian, Latin, Spanish, and Greek, in addition to her native Scots.

[42] Portraits of Mary show that she had a small, oval-shaped head, a long, graceful neck, bright auburn hair, hazel-brown eyes, under heavy lowered eyelids and finely arched brows, smooth pale skin, a high forehead, and regular, firm features.

[44] Mary was eloquent, and especially tall by 16th-century standards (she attained an adult height of 5 feet 11 inches or 1.80 m);[45] while Henry II's son and heir, Francis, stuttered and was unusually short.

Under the Third Succession Act, passed in 1543 by the Parliament of England, Elizabeth was recognised as her sister's heir, and Henry VIII's last will and testament had excluded the Stuarts from succeeding to the English throne.

Yet, in the eyes of many Catholics, Elizabeth was illegitimate and Mary Stuart was the rightful queen of England, as the senior surviving legitimate descendant of Henry VII through her grandmother, Margaret Tudor.

[54] Two of the Queen's uncles, the Duke of Guise and the Cardinal of Lorraine, were now dominant in French politics,[55] enjoying an ascendancy called by some historians la tyrannie Guisienne.

[72] Modern historian Jenny Wormald found this remarkable and suggested that Mary's failure to appoint a council sympathetic to Catholic and French interests was an indication of her focus on the English throne, over the internal problems of Scotland.

Mary's numbers were boosted by the release and restoration to favour of Lord Huntly's son and the return of James Hepburn, 4th Earl of Bothwell, from exile in France.

Not content with his position as king consort, he demanded the Crown Matrimonial, which would have made him a co-sovereign of Scotland with the right to keep the Scottish throne for himself, if he outlived his wife.

[111] In October 1566, while staying at Jedburgh in the Scottish Borders, Mary made a journey on horseback of at least four hours each way to visit the Earl of Bothwell at Hermitage Castle, where he lay ill from wounds sustained in a skirmish with John Elliot of Park.

[119] Divorce was discussed, but a bond was probably sworn between the lords present to remove Darnley by other means:[120] "It was thought expedient and most profitable for the common wealth ... that such a young fool and proud tyrant should not reign or bear rule over them; ... that he should be put off by one way or another; and whosoever should take the deed in hand or do it, they should defend.

[133] A week later, Bothwell managed to convince more than two dozen lords and bishops to sign the Ainslie Tavern Bond, in which they agreed to support his aim to marry the queen.

Historian Jenny Wormald believes this reluctance on the part of the Scots to produce the letters and their destruction in 1584, whatever their content, constitute proof that they contained real evidence against Mary.

[180] In Fraser's opinion, it was one of the strangest "trials" in legal history, ending with no finding of guilt against either party, one of whom was allowed to return home to Scotland while the other remained in custody.

[189] Her chambers were decorated with fine tapestries and carpets, as well as her cloth of state on which she had the French phrase, En ma fin est mon commencement ("In my end lies my beginning"), embroidered.

[195] In May 1569, Elizabeth attempted to mediate the restoration of Mary in return for guarantees of the Protestant religion, but a convention held at Perth rejected the deal overwhelmingly.

[198] Elizabeth's principal secretary William Cecil, Lord Burghley, and Sir Francis Walsingham watched Mary carefully with the aid of spies placed in her household.

[199] In 1571, Cecil and Walsingham (at that time England's ambassador to France) uncovered the Ridolfi Plot, a plan to replace Elizabeth with Mary with the help of Spanish troops and the Duke of Norfolk.

Pope Gregory XIII endorsed one plan in the latter half of the 1570s to marry her to the governor of the Low Countries and illegitimate half-brother of Philip II of Spain, John of Austria, who was supposed to organise the invasion of England from the Spanish Netherlands.

She was concerned that the killing of a queen set a discreditable precedent and was fearful of the consequences, especially if, in retaliation, Mary's son, James, formed an alliance with the Catholic powers and invaded England.

[236] When the news of the execution reached Elizabeth, she became indignant and asserted that Davison had disobeyed her instructions not to part with the warrant and that the Privy Council had acted without her authority.

[244] Assessments of Mary in the 16th century divided between Protestant reformers such as George Buchanan and John Knox, who vilified her mercilessly, and Catholic apologists such as Adam Blackwood, who praised, defended and eulogised her.