John Lindsay, 5th Lord Lindsay was made an Extraordinary Senator of the College of Justice on 27 June 1532. John, an Extraordinary Lord of Session in 1541, was present at the trials of Sir John Borthwick (for heresy) and James Hamilton of Finnart (for treason). John witnessed the death of James V at Falkland Palace. In 1543, John Lindsay and seven other lords took custody of the infant Mary, Queen of Scots, and conveyed her from Linlithgow Palace to Stirling Castle. 264. John was one of the commanders at the Scottish victory against England at the battle of Ancrum in 1545. During the Scottish Reformation,
Mary, Queen of Scots took her into protective custody at Carlisle Castle. Mary apparently expected Elizabeth to help her regain her throne. Elizabeth was cautious, ordering an inquiry into the conduct of the confederate lords and the question of whether Mary was guilty of Darnley's murder. In mid-July 1568, English authorities moved Mary to Bolton Castle, because it was further from the Scottish border but not too close to London. A commission of inquiry, or conference as it was known, was held in York and later Westminster between October 1568 and January 1569. In Scotland, her supporters fought a civil war against Regent Moray