In 1638, the year after the Prayer Book Riot in St Giles, a manifesto known as The National Covenant was drawn up, protesting against Charles I’s ecclesiastical policies in Scotland. It pledged those who signed it to ignore his intended changes unless these were approved by the General Assembly of the Church of Scotland. It was composed by Alexander Henderson, who would the following year become one of the St Giles’ ministers, and Archibald Johnston of Wariston, an advocate who was a member of the congregation. Signed on 28 February 1638 in the nearby Greyfriars Church by leading nobles and barons, parchment copies were intended to be circulated for signature to every burgh and parish in Scotland. Many of these documents have been preserved, including the Linlithgow copy which was presented to St Giles’ by Alexander Wallace W.S. in 1926 and is displayed in the Preston Aisle in a special wooden stand.
Armed conflict swiftly followed in 1639, with The Bishops’ Wars, and the King’s opponents were originally known as Covenanters, although later they split into separate groups. During the subsequent Civil War, a captured royalist named Sir John Gordon of Haddo was imprisoned in a room above the North Porch of St Giles’ before his execution just outside. The prison came to be known as Haddo’s Hole. After the Restoration of Charles II, a group of Covenanters continued to oppose royal policies and were defeated at the Battle of Rullion Green in 1666. Some were then imprisoned in Haddo’s Hole, before being executed, deported or released.