The two succeeding regents, Lord Lennox, grandfather of King James, and Lord Erskine, the Earl of Mar, served only a brief period. Lord Lennox was assassinated in 1571, and Lord Erskine died shortly after assuming the position of regent in 1572. Following these deaths, the Earl of Morton assumed the regent's seat, which he would hold until 1587, though his influence was evident until his death in 1591.
Morton was a strong Protestant but was closely tied to the English. He envisioned the church along much more Anglican lines, and this distressed the Reformed Presbyterians. Despite this difference, when Knox died in 1572, just two days after Morton became regent, Morton reflected, "There lies one who neither feared nor flattered any flesh." With Knox now out of the way, the advantage fell to Morton. He began his Anglican changes by introducing the "Tulchan Bishops" into the government of the church. The common title came from detractors who used "tulchan" to describe the straw-stuffed calf skins used to trick cows into producing milk; they saw the new bishops as similarly misleading the people into the episcopal way.
The Reformed Kirk was compelled to abide by these episcopal innovations because the King, now fourteens years old, had come under the persuasive influence of Lord D'Aubigny, a Frenchman believed to be an agent for both France and Roman Catholicism.
Many believed that the Reformed Kirk was doomed. This sentiment increased when Morton ceased serving as regent in 1587, and D'Aubigny was appointed Lord High Chamberlain and Duke of Lennox. D'Aubigny openly aimed to destroy all Scottish ties to England, but he needed to remove Morton from the scene completely in order to accomplish this goal. He ultimately achieved this goal by falsely linking Morton to the death of Lord Darnley, the King's father. Morton was executed, and D'Aubigny now had control and the King's ear.
Many Protestants had long viewed D'Aubigny with suspicion, and the Morton incident confirmed their fears. In response to D'Aubigny's actions, the General Assembly instructed John Craig, a colleague of John Knox, to draft a Protestant confession of faith, which would later serve as the basis for the National Covenant. The Protestants not only formulated a new confession, they also entered into the King's Covenant of 1581. This covenant bound the parties to uphold the King and the true religion against all usurpation.
Nevertheless, the King's counselors still controlled the young King. In 1583, a group of Protestant Lords attempted to break this control by kidnapping the King. This group, the "Ruthven Raiders," received their designation from the Ruthven Covenant of 1582, to which they had bound themselves. This covenant read as follows:
We, underscribing, considering the present danger apprehended to the ministers and professors of God's true religion within this realm, the peril of the King's Majesty's own estate and crown, and of such as have been obedient to his authority, and the abuse and confusion of the Commonwealth in all estates: being therefore of necessity moved, to come and remain with his Majesty, until the time that remedy and reformation of the same be provided; therefore, in God's fear, and in his Majesty's obedience, we have avowed and sworn, and by the tenor hereof faithfully bind and oblige us to another, that we shall concur in resisting of the evils intended by whosoever persons, against God's true religion, the person and authority of the King's Majesty, our Sovereign Lord, and ourselves, in seeking and providing redress and reformation of the enormities and abuses in the Commonwealth, to the establishing of the same true religion, and reformation of justice, good order and quietness to the own integrity, according to the Word of God, and loveable laws and customs of this realm: and shall take honest, true, and plain part with others esteeming, reputing, and holding all suddanties and occasions that have fallen, or shall fall out against any one of us, in particular, and all enterprises attempted by any one of us, in prosecution of this honest, godly, and lawful cause, to be common to us all, without shrinking therefrom, for any thing that may be opposed to the contrary, for any past offence or quarrel among ourselves as we will answer to the Eternal God, our due obedience to the King's Majesty our Sovereign, and upon our honour, faith, and truth. Over two dozen Lords had affixed their names and lives to this covenant.
After kidnapping James VI, the Ruthven Raiders held him for two years until he finally was able to escape. Shortly after he returned, Sir John Maitland successfully negotiated a treaty, the "Protestant League," which would later become the foundation of a common Protestant union between the two countries.
James VI, however, held to a Divine Right view of his authority, and thus stationed himself as the supreme head of both state and church. This absolutist commitment set him in direct conflict with the Reformed Kirk of Scotland and Knox's successor, Andrew Melville.
The General Assembly appointed Melville as Principal at the College of Glasgow, where he quickly gained prominence. Morton, recognizing Melville's growing influence, tried to persuade him to adopt episcopacy and offered him a large benefice in Grovan. Melville refused. Later the General Assembly appointed him to the Chair of Theology and Principal at St. Andrews, where he served for many years.
Melville was well aware of the threats against the Reformed Kirk. In 1582, He declared before the General Assembly that the King's party intended, "to pull the crown from Christ's head, and wrest the Sceptre out of His hand." Moreover, the Assembly sent several protests to James VI and His Council, expressing their concerns and seeking redress. At one point, the Earl of Arram, one of the King's party, became enraged by their actions and retorted, "Is there any here that dare subscribe to these articles." Melville and his fellow-laborers took the challenge and boldly replied, "We dare and will render our lives in the cause."
Later, in February of 1584, Melville was called before the court of James VI and accused of preaching against the King and his authority from Daniel 4. Even though the Earl of Arram, who prosecuted the case, failed to provide sufficient evidence to make his case, the court ordered Melville to prison in the Edinburgh castle. Melville later escaped with the help of some friends and went into hiding for two years. The acting Archbishop, Patrick Adamson, appointed by the king, excommunicated Melville, which infuriated the populace. Melville was later able to return to St. Andrews, when the Synod of Fife excommunicated Adamson for immorality.
The King's court, dismayed by the continuing actions of the General Assembly, overturned the independence of the church by passing the Black Acts in 1584, which prohibited any ecclesiastical assembly to meet without the King's consent and required that all ministers were to accept the rule of the bishops of the church.
Throughout this time, Melville found himself in conflict with the King. Melville often served as a representative of the ministers before the King who at one point inquired, "Who sent for Melville?" Melville replied, "Sire, I have a call to come from Christ and His church, who have a special concern in what you are doing here, and in opposition to whom Ye are here assembled; but be Ye assured, that no counsel taken against Him shall prosper; and I charge you, Sire, in His name, that you and your Estates here convened favor not God's enemies, whom He hateth."
Shortly following these events, the Act of 1592 passed which reestablished presbyterianism in Scotland. The Act called for a church government made up of synods, presbyteries, and local sessions, the abolishment of episcopal restrictions and bishops, remuneration of ministers, and confirmed all the liberties for the true church of Christ. 
Protestant people and leaders viewed these turn of events as favorable to their cause, and all seemed to be going well until Philip of Spain attacked England. Scottish nobles had plotted with Philip in this invasion, and James VI was called upon to take action. First, James exiled the responsible nobles but later allowed them to return, much to the furor of many. Melville reminded James at a 1596 assembly that he as King "was God's silly vassal and that there are two kings and two kingdoms in Scotland. There is Christ Jesus the King, and His kingdom the Kirk, whose subject King James VI is, and of whose kingdom, not a king, nor a lord, nor a head, but a member he was." 
James realized that if there were no bishop, there would be no king. He had to act. He summoned a preacher, David Black, for allegedly preaching sedition. Black was a protegé of Melville and refused to appear arguing that the King had no jurisdiction over the pulpits of the Kirk. The King had Black arrested and tried in Edinburgh. The people of the city revolted and the King threatened to harshly sanction the people if they did not banish all ministers who opposed the King. The city council complied and the time of peace ended.
One immediate drawback of the Act of 1592 was that it granted the King the power to designate the meeting location of the yearly General Assembly. James used this to his advantage. He would designate the time and location of assemblies which best served his own ends.
James gained the most advantage when he ascended to the English throne in 1603. With the help of the English church, he could secure greater control in Scotland. In 1606, Melville was called to London, and two bishops attempted to persuade him of the superiority of episcopal government, but Melville remained undaunted. Bancroft, the Archbishop of Cantebury, successfully persuaded the King to banish Melville from the realm, and Melville was exiled to Sedan in France, where he spent his remaining years teaching at a Huguenot seminary.
In Scotland itself, James reestablished bishops in the Scottish church and exiled many leading Presbyterians. In 1618 he established the Articles of Perth which once again patterned the worship of the Scottish Kirk after the English model. The Articles required, among other items:
1) That the sacrament of the body and blood of Christ should be received kneelingJames appeared to have won the war, but he seriously underestimated the commitment of the Scottish people. Instead of bequeathing his son, Charles I, a realm in submission, he gave him a kingdom tensing for a fight. In a few short years, the Scottish people would rise and willingly seal their commitment with their blood. The Scottish people would see God move remarkably in their midst, glorifying their blessed King Jesus.
2) That the sacrament might be administered to the sick privately
3) That baptism might by administered in private homes where necessary
4) That children of eight years of age should be confirmed by the Bishop
5) That holidays be established for the birth, passion, resurrection, and ascension of the Lord, and for the sending of the Holy Spirit. 
 J.H.S. Burleigh, A Church History of Scotland, (London: Oxford Univ., Press, 1973), p. 34.
 Ibid, p. 196.
 John Lunsden, The Covenant of Scotland, (Paisley: Alexander Gardner, 1914), p. 116.
 J. Howie, The Scots Worthies, (Edinburgh: Oliphant, Anderson, and Ferrier, 1775), p. 91.
 Ibid, p. 92.
 Ibid, p. 94.
 Ibid, p. 95.
 Burleigh, Church History, p. 204.
 Ibid, pp. 204-205.
 Ibid, p. 207.
 Ibid, p. 208.