On the 28th February 1638, a petition was signed by a group of nobles, church elders, lawyers and ordinary men. The petition, called the Covenant, demanded King Charles I to rein back on some of the changes he was making on the practice and doctrine of the church in Scotland. Since James VI, the Church of Scotland was finding the monarchy was introducing practices which were increasingly at odds with the church's Presbyterianism. One of the principle issues was the role of the bishops in Scotland; the church in Scotland had little place for bishops, and so Charles' insistence on their central role within the church was considered far too Catholic.
The last straw came in 1647 when Charles introduced a new Prayer Book to Scotland. In an attempt to bring back peace to the city, the Covenant was drawn up, reminding the King of his position within the church. Copies were made and sent to every parish in Scotland, and there was a rush for everyone to sign it. There are legends that such was the religious zeal of the time that many signed in their own blood, but there were also many who were forced into signing, probably against their wish.
While it was intended as a peaceful petition, the Covenanting movement quickly picked up momentum, and by 1640, had not only set up their own Assembly, but also raised an army and marched into England. Combined with Charles' own disputes with the Parliament in Westminster, it wasn't long before civil war broke out in Scotland and England, and eventually, Ireland. By the end of the war, the monarchy had been abolished and Oliver Cromwell had become Lord Protector of the Commonwealth.
The 1650s saw continued fighting. Now the Covenanters were fighting with Cromwell in order to spread their church throughout England as well as Scotland. Charles' son was declared King Charles II in Scotland in 1651 only after having accepted the terms of the Covenant, but was eventually defeated and forced into exile. For a brief while, relative peace returned under the Commonwealth.
The peace however was short lived, and once the monarchy was restored in 1660, Charles II quickly went back on his word. Bishops were re-introduced into Scotland, and any ministers against this were outlawed. The Covenanters grew in numbers, particularly in the South West of Scotland, where illegal outdoor meetings, or conventicles, numbered sometimes into the thousands. There were several organised Covenanting rebellions, with limited and short lived success. Many of those taken prisoner were kept in the Covenanters' Jail in Greyfriars Kirkyard. Only with the Glorious Revolution of 1688 and the accession of the Protestant William of Orange to the throne did the various groups in Scotland meet a degree of compromise. Nevertheless, many continued to be dissatisfied and formed increasingly radical sects or emigrated to the New World.