Charles and Laud had long resented the independence of the Presbyterian Church of Scotland. They wanted to bring it more into line with the Laudian Church of England and aimed to reform its practices and prayer-book. In particular, Charles feared the Presbyterian dislike of bishops. Bishops were part of a hierarchy of church and state that led ultimately up to the King as Supreme Head of the Church. Any attack on any part of that chain was a diminution of the King's authority. James I had once perceptively warned, 'No Bishop, No King.'

Charles challenged Scottish independence with the introduction of a new Prayer Book. It was to set the three kingdoms on a collision course far faster than Charles could control. England, prosperous and at peace in 1637, was about to ignite the War of the Three Kingdoms. The so-called English Civil War began in Scotland. The catalytic event which ignited all subsequent conflict occurred in St. Giles Cathedral in Edinburgh in 1637.

On July 23rd 1637, the Scottish ecclesiastical establishment was gathered together in all its pomp at St. Giles Cathedral, Edinburgh to partake of Sunday service according to the new Prayer Book designed by Laud and Charles. As soon as the Dean of the Cathedral began to read from the book, he was shouted down by a chorus of women 'of the meaner sort'.

They proceeded to break up the service, shouting loudly 'the mass is come amongst us!'. When the Bishop of Edinburgh climbed the pulpit to appease the mob he was met with a volley of Bibles and then a stool flung from the back by another woman which only just missed him. The bailiffs poured down from the gallery in an attempt to restore order. But across Scotland, congregations reacted with similar fury to the new service. In Glasgow, a minister was almost torn to pieces. The Bishop of Brechin adopted a more ruthless approach- by conducting the service over a pair of loaded pistols.

Across Scotland antagonism towards the prayer book hardened into a full-scale rebellion against the King. In February 1638, a group of leading Scottish nobles, clergy and gentry met at Greyfriars Kirk in Edinburgh to sign the National Covenant, a document which promised to defend the Presbyterian Scottish Church against any attempt by Charles to introduce the English Prayer Book, the Anglican liturgy or bishops jure divino (the Scots Presbyterians had no opposition to bishops serving as administrators).

Copies of the Covenant travelled the length and breadth of Scotland and many more signed up. Although the Covenant urged loyalty to the King, it was a profound declaration of Scottish national pride and a testament to the Scots' desire to defend their Kirk. Defending the Church and remaining loyal to Charles might prove to be incompatible.