Not even the execution of his mother in 1587 was sufficient to rouse him to take serious action. Though he was urged by many of the Scottish nobles to declare war he contented himself with angry speeches and protests that passed unheeded. Even many of the Presbyterian lords were ready to support him had he declared war, and Catholic noblemen like the Earls of Huntly, Erroll, and Crawford, Lord Maxwell, and Lord Hamilton, offered their assistance. It was well-known, too, that Philip II. was preparing at the time for an invasion of England. Had Scotland declared war the results might have been disastrous for England, but James, instead of taking the offensive, accepted a pension from Elizabeth and offered to assist in the defence of the kingdom. He endeavoured at first to conciliate the Catholic party by restoring John Leslie Bishop of Ross, who had been for years a most zealous defender of Mary Queen of Scots, to his See and his possessions, and by appointing the exiled Archbishop of Glasgow to be his ambassador at the French court. The General Assemblies, however, backed up by Elizabeth forced him to take strong measures against the adherents of the old religion. In 1593 a proclamation was issued ordering all Jesuits and seminary priests to leave Edinburgh within two hours under pain of death, and a violent campaign was begun in nearly every part of Scotland against the Catholic nobles and clergy.
The Catholic lords who were in close communication with Spain were forced to take up arms. Their forces were mustered under the Earls of Huntly and Erroll, and gained a complete victory at Glenlivet over the Earl of Argyll who was dispatched against them. When the news of this defeat reached the king at Dundee he displayed unwonted activity. He assembled a large army to punish his rebellious subjects, and the Catholic lords were at last forced to make their escape from the country. With the flight of Huntly and Erroll (1595) and the dispersal of their troops the triumph of Protestantism in Scotland was assured.
The great leader in the attack on the Catholic Church in Scotland was John Knox who belonged to the Geneva school, and who worked hard for the introduction of the Calvinist system of Church government. The state of affairs in Scotland at the time was very favourable to his designs. Obviously there could be no question of royal supremacy or of a State Church being established after the English model, since the Queen of Scotland was a staunch supporter of the Roman Church. Neither could the principle of parliamentary control be accepted since the Scottish Parliament was comparatively powerless. Had the revenues and possessions of the Scottish bishoprics and ecclesiastical benefices been left untouched the democratic form of government would have been impossible, but as the hungry lords of Scotland had appropriated already the wealth of the Church they had no special interest in the ecclesiastical appointments. The result was that the General Assemblies, composed of both preachers and laymen, became the recognised governing body of the new religion, and they arrogated to themselves full control of ecclesiastical affairs. The bishops who were willing to conform were not, however, removed from office. They were subjected to the control of the General Assembly, and were placed on the same level as the recently named superintendents.
But the regents who governed Scotland during the minority of James VI.
were not inclined to receive with favour the idea of ecclesiastical independence. In 1571 the Earl of Mar insisted on appointing an archbishop to St. Andrew's without reference to the General Assembly, and immediately the preachers were up in arms. They were handicapped in their resistance by the fact that their great leader Knox was too ill to afford them much assistance, and at last they were forced to accept a compromise according to which the old system of ecclesiastical government was left practically untouched. Archbishops, bishops, deans and chapters were retained; the bishops were to be elected by the chapters with the permission and approval of the king and were to receive the temporalities by royal grant; and all persons admitted to benefices were to promise obedience to their bishops. At the same time it was agreed that the bishops should be subject to the General Assemblies in spiritual matters, as they were subject to the king in temporals. It was hoped that by means of this compromise peace might be secured, but in a short time the attack on episcopal government was renewed with still greater vigour. A new leader had appeared in the person of Andrew Melville, the Principal of the College of Glasgow, and the friend of the great Swiss Reformer, Beza.
Despite the fact that the regent espoused the cause of episcopacy the General Assemblies were determined to continue the struggle for its overthrow. The adoption in 1580 of the /Second Book of Discipline/, involving as it did the overthrow of episcopal authority, the rejection of state interference and the assertion that spiritual authority was derived only from the people, was a severe blow to the young king and his advisers; but they found some consolation in the fact that the Scottish Parliament re-asserted the principle of royal supremacy and recognised the authority of the bishops (1584).