She married her first cousin Henry Stewart, Lord Darnley on 29th July 1565.
Scotland: The Final Years
This marriage was unacceptable to the Protestants, and Moray, with the aid of other nobles, raised a rebellion which Mary quickly suppressed. Nevertheless she felt betrayed by her Protestant advisors and withdrew some of her support from the Reformed church. Her marriage with Darnley soured and she refused him the right to succeed if she died without issue. Alone and disappointed, Mary turned to her Italian secretary, David Rizzio, for comfort and advice. The Protestant lords disliked Rizzio's influence because they suspected him of being a papal agent, and Darnley openly stated that the Italian was too intimate with the Queen. On 9th March 1566 a group of Protestant lords, acting with the support of Darnley, murdered Rizzio in Mary's presence at Holyrood Palace. Mary, who was six months pregnant, survived the horrible ordeal. In Edinburgh Castle on 19th June 1566, estranged from her husband and his allies, she gave birth to a son James (later James I of England). By the end of 1566 Mary had befriended James Hepburn, Earl of Bothwell, and was seeking a way to dissolve her marriage with Darnley. Various schemes were concocted; it seems unlikely, however, that Mary was aware of the actual plot to eliminate her husband. On 10th February 1567 Darnley was murdered at Kirk o' Field; the circumstances of his death to this day remain a mystery. At the time, Bothwell was believed to be the chief instigator. Nevertheless he was acquitted after an all too brief trial. In April, Mary went off with Bothwell (perhaps a victim of abduction); early in May he obtained a divorce from his wife, and on 15th May 1567 he and Mary were wed according to the Protestant rite. These events alienated even some of Mary's closest supporters. The nobles, many of whom disliked Bothwell, banded together to face Mary and her new husband at Carberry. The Queen was forced to surrender, and Bothwell fled. Mary was imprisoned at Lochleven Castle and on 24th July 1567, she was compelled to abdicate in favour of her son who became King James VI of Scotland. With the help of a few brave friends, Mary escaped from the castle and immediately rallied a large force behind her. They engaged in battle at Langside on 13th May 1568, and were soundly beaten by the army led by the Protestant lords. At this point Mary decided to leave Scotland and go to England to beg support from her cousin Elizabeth.
England: The Captive Years
Mary crossed the Solway into England and nearly 19 years of captivity; she never returned to Scotland.