Mary Stuart was born at Linlithgow Palace in West Lothian, Scotland. She was the daughter of James V, king of Scotland and Mary of Guise, from France. James V died a week after Mary was born and she became Queen of Scotland. The young Queen's safety was threatened by Earl of Arran who assumed the regency of Scotland. To ensure her safety, Mary of Guise took the child to Stirling Castle and never left her side.

After a lengthy siege failed to take the well defended castle at St. Andrews, Mary of Guise asked the French for help. The castle at St. Andrews was captured and the Protestant leaders and John Knox were taken into custody.

The request of the Scottish Regent, Mary of Guise, for help to fight the English was answered by the arrival of an army of several thousand French. The assistance came on condition that her daughter Mary Stuart should marry the French Dauphin, Francis.

A group of Scottish Lords signed a covenant promising to support the advancement 'the most blessed Word of God' and to push forward the Reformation in Scotland. This was a move against what they saw as the threat from France which came from the marriage of Mary, Queen of Scots to the French Dauphin. They called themselves the Lords of the Congregation.

In Scotland, the regent, Mary of Guise had designs to place put her daughter Mary on the throne of England. There were many Protestants in Scotland and Queen Elizabeth had been secretly helping them in their opposition of the regent and her daughter. There were fears in Scotland that Mary of Guise, a devote Catholic, would secure French assistance and make Scotland a French territory, The Lords of the Congregation, who by now now were a powerful force in Scotland, pushed for an agreement with England that English help would be provided against a French invasion. Queen Elizabeth agreed to this and the treaty was signed at Berwick by the Scots and the Queen's representative, Thomas Howard, Duke of Norfolk.

Mary Stuart's mother, Mary of Guise, died in Scotland leaving the country in a state of civil war.