James V died in 1542 after the battle of Solway Moss. The crown passed to his newly-born daughter, Mary. King Henry VIII of England wanted Mary to marry his young son Edward, and when the Scots refused, he began the 'rough wooing' campaign - destroying Scots towns, villages and churches. I.M.M. McPhail's Dumbarton Castle tells of a curious ordinance of Henry VIII: "A memorandum drawn up in preparation for an English invasion of Scotland in 1542, containing distances between towns, mentioned 'the strongest castle in Scotland called Dumbretton; here St Patrick was born and by his petition there should never be horse dung in it' ", an early English acceptance of the Dunbartonshire claim to St. Patrick's birthplace.
Although Mary of Guise, the Queen Mother and regent, conceded Drumry to the Semples in 1545, the Craufurds remained pro-Queen Mary. Thomas Craufurd fought against the English in the Battle of Pinkie in 1547. Captured and later released, he joined the court of Queen Mary in France. (Mary was sent to France for her safety in 1548.)
The Reformation was taking hold in Scotland and Mary of Guise sent for French troops to quell unrest. The troops were based in Leith. In France, Queen Mary had married the French heir to the throne, later King Francis II. The Scots were uneasy about the growing French power over Scotland and asked the English for help. Queen Elizabeth sent 9000 men to relieve Leith and ended the Auld Alliance with the Treaty of Edinburgh in 1560. Parliament declared Scotland legally Protestant. In the spirit of the Declaration of Arbroath this meant that the people had the right to choose their religion regardless of the current monarch. Sovereignity was seen to lie with the people.
King Francis II died at the end of the year, and Queen Mary returned to Scotland in 1561, aged 18. She married Henry, Lord Darnley, the heir to the English throne. Thomas Craufurd became his equerry. John Craufurd was granted Drumry in 1567.
Darnley became jealous of David Rizzio, the Queen's Italian secretary and had him murdered in 1566. In 1567, as he was recovering from syphilis, he was strangled and his house was blown up with gunpowder. This incensed Thomas Craufurd who took the side of Regent Moray against Mary at the Battle of Langside.
Mary married James Hepburn, the Earl of Bothwell, the prime suspect of Darnley's murder. At this she was imprisoned at Loch Leven castle; Bothwell escaping to become a pirate. She was forced to abdicate in favour of her son, King James VI.
Mary escaped and raised some forces, among them Thomas Craufurd's brother, Hew of Drumry, and probably the Hamiltons and Galbraiths from Drumchapel and surrounding areas. The Battle of Langside was fought in 1568, only 6 miles away from Drumchapel, and the Regent Moray was victorious.
Now defeated in Scotland, Mary asked for mercy from her rival and cousin, Queen Elizabeth in England. She was kept in prison for 20 years but was found guilty of plotting against the Protestant queen - Thomas Craufurd was a witness at the trial - and executed at Fotheringay Castle in 1587.