[6] His family supported Mary, Queen of Scots, even after her imprisonment at Lochleven Castle, her abdication in favour of her one-year-old son on 24 July 1567, her defeat at Langside in 1568 and her flight to England shortly afterwards.
In 1570 Moray, who was regent during part of the minority of King VI, was assassinated by John Hamilton of Bothwellhaugh, a supporter of Queen Mary, at Linlithgow.
[27] John, with Angus, the Earl of Mar, and the Master of Glamis and with the connivance of Elizabeth I of England, raised an army and entered Scotland, reaching Stirling in October 1585.
[28] At a parliament convened at Linlithgow on 1 December 1585, King James rescinded Hamilton's forfeiture and restored him and the other lords to their previously held lands.
[29] According to David Hume of Godscroft, the Earl of Angus and Hamilton argued over precedence in the king's privy or outer chamber at Holyrood Palace.
[32] On 1 July 1592 Lord John Hamilton captured Archibald Wauchope of Niddrie with other rebel followers of the Earl of Bothwell at the meadow of Lesmahagow and imprisoned them in Craignethan Castle, promising their lives would be spared.
James VI sent Sir John Carmichael, captain of the royal guard, to collect the prisoners, but one of Hamilton's sons released them.
Although James had earlier made Hamilton captain of the castle 'for life', it was an office which Lennox coveted and he lobbied the king hard for it.
[37] In August 1602 he hosted the French ambassador, the Baron de Tour at Hamilton Palace, who hunted with the king and the Duke of Lennox and played a card game called "mawe".