Scottish Reformer and
founder of Presbyterianism in Scotland

John Knox was born at Haddington in East Lothian in about 1505. His father was William Knox. He obtained a liberal education in grammar school, and at the age of sixteen he was sent to pursue his studies at the University of Glasgow, where Dr. John Major was professor of philosophy and theology. Majors, also a native of Haddington, was one of the leading intellectuals of Europe, and was previously the foremost scholastic theologian at the University of Paris. Unlike the ordinary teachers of theology, he did not lecture only on Peter Lombard's Books of the Sentences (the leading textbook of Scholastic Theology), but introduced his students to the text of the Latin Bible. Beza says that Knox began to study with such proficiency that it was thought he would one day become a better schoolman than his master, Majors, but after reading the works of St. Jerome and St. Augustine, he realized the errors in the conventional teaching (scholasticism was at its height, studies often focused on absurd arguments, such as, "how many angels could dance on the head of a pin?"). He left the university without obtaining a masters degree, and taught in some capacity at the University of St. Andrews. It appears that he took the orders of the Catholic priesthood in about 1530 and served with some religious establishment for the next 10 years in Haddington, functioning as a notary (this was a task of churchmen in the middle ages, our word "clerk" comes from cleric) and as a private tutor.

Protestant "heresy" first appeared in Scotland at the beginning of the fifteenth century, when followers of Wycliffe (called Lollards) fleeing from persecution in
 England, found their way across the border. In 1433, a Czech named Paul Crawan, a follower of John Huss, was arrested while studying at St. Andrews University, and burned as a heretic. The fires of Protestantism which Luther started in Germany came to Scotland from the German coastal towns, entering through the eastern port cities of Scotland; Leith, Montrose, and Dundee. Within 10 years of the posting of the 95 theses in Wittenburg, Protestant tracts were being smuggled into Dundee, including Tyndale's English translation of the New Testament (which was published in Germany).

There was at St. Andrews University, at about the same time as John Knox, a man named George Wishart, who later fled to England to avoid persecution of the Catholic rule in Scotland. Ironically, while preaching in Bristol, he was denounced by King Henry VIII's Church of England as a heretic. He recanted (of what we're not sure, but it may well be that Mr. Wishart was an early forerunner of the Puritans). He returned to Scotland, and preached the gospel in various cities and towns. By 1545, persecution in Scotland was growing and Wishart was warned by the protestant landowners (lairds) to stop preaching and lie low for a while. Wishart refused, but prophesied that he would soon be captured and burnt. A group of lairds decided to protect him from the authorities, and grant him safe conduct, as he traveled for four weeks from town to town, entering churches without authority, and preaching to large crowds. Knox, still a Catholic priest, was employed as a tutor for the sons of one of these lairds and accompanied the group protecting Wishart, carrying with him a large double-edged sword. As the danger grew, the group diminished, and Wishart exhorted the rest to leave him and escape danger. Knox did not wish to leave him, asking to stay with him til the end, but Wishart replied, "Nay, return to your home and God bless you. One is sufficient for a sacrifice." Soon afterwards, Wishart was arrested, taken to St. Andrews, condemned as a heretic and burnt at the stake. The martyrdom of Wishart in 1546 was the turning point in the spiritual life of Knox, causing him to renounce Catholicism and to profess his adherence to the Protestant faith.

The English and the Scottish Protestants reacted very differently to persecution. In England, submission to authority was maintained, even to the flames of martyrdom. But in Scotland, Cardinal Beaton, (the churchman considered most responsible for the death of Wishart) was to meet with a bloody retribution for his merciless enforcement of the law. Knox writes in his History of the Reformation in Scotland:

"men of great birth, estimation and honour, at open tables avowed, that the blood of the said Master George should be revenged, or else they should cast life for life."

On May 29, 1546, party of sixteen young gentlemen broke into St. Andrews Castle, after killing the sentry at the gate, and stabbed Cardinal Beaton to death. After insulting his corpse, they hung the body over the castle wall for the inhabitants of St. Andrews to see, and held the castle against the government. This sordid affair was the beginning of the Protestant revolt in Scotland. Knox has often been denounced by his critics for his attitude to the death of Beaton. He describes the murder in his History, concluding with the words, "These things we write merrily." A more sober comment of his on the murder was:

"These are the works of God, whereby He would admonish the tyrants of this earth, that in the end He will be revenged of their cruelty, what strength so ever they made in the contrary."

Whether he actually approved of the means by which these "works of God" were carried out can only be inferred by the fact that he never wrote a disapproving word of the deed. Because of his ties with Wishart, he considered himself in danger and resolved to leave Scotland, but Cockburn of Ormiston, whose sons John Knox was tutoring, convinced him to enter the castle of St. Andrews as a place of safety. It was there that he received a public call to the ministry, "whereat", to use his own words, "said John, abashed, burst forth in moist abundant tears and withdrew himself to his chambers." In June of that year, the Catholics of Scotland and France joined their forces to avenge the death of Cardinal Beaton by capturing the Protestant garrison of St. Andrews. It was stipulated that the lives of the refugees should be spared, that they should be removed to France, and that those who declined to serve in the French army should be conveyed to any other country except Scotland. Knox, sharing the fate of his companions at the Castle of St. Andrews, was conveyed on board one of the French ships to Rouen, France.

The terms of the surrender were grossly violated, and the captives were treated as prisoners of war. Knox and some of the others were consigned to life-time sentences as galley slaves. Here they were subjected to much suffering and humiliation, but despite hardship and threats, none of them renounced their faith.

In the winter of 1548, Henry Balnaves, a fellow Scottish protestant captured at St. Andrews and then imprisoned in the old palace of Rouen, sent Knox the rough draft of a treatise on the doctrine of justification by faith for his perusal. He carefully revised it, adding chapter divisions, and a summary, and had it sent to Scotland for publication with an epistle addressed by "the bound servant of Jesus Christ unto his best beloved brethren of the congregation of the Castle of St. Andrews, and to all professors of Christ's true evangel."

In February 1549, after an imprisonment of 19 months, Knox obtained his release from the French galleys. Since he probably obtained his freedom due to the intercession of King Edward VI or the English government (they had been negotiating for the release of English and Scottish protestant prisoners in exchange for French prisoners), he came to London, and was favorably received by Archbishop Cranmer and the lords of council. He remained in England for five years, during which time he was first appointed preacher to Berwick, then to Newcastle.

At Berwick, where he labored for two years, he preached with his characteristic fervor and zeal, exposing the errors of Romanism with unsparing severity. Although Protestantism was the official position of the Church of England since the reign of Henry VIII, there were many loyal Roman Catholics (papists), even in the high ranks of the clergy. The bishop of John Knox's diocese, Dr. Cuthbert Tunstall, was an avid Catholic. Knox was accused of asserting that the sacrifice of the Mass is idolatrous, and was cited to appear before the bishop to give an account of his preaching. On April 4, 1550, Knox entered into a full defense of his opinions, and with the utmost boldness proceeded to argue that the mass is a superstitious and idolatrous substitute for the sacrament of the Lord's Supper. (vol. 3 of History 54,-56). The bishop did not venture to pronounce any ecclesiastical censure.

The fame of the preacher was only extended by this feeble attempt to restrain his boldness. From a manuscript discovered in the 1870's titled, "The practice of the Lord's Supper used in Berwick by John Knox, 1550," we now know that the very beginning of Puritan practice in the Church of England in the administration of the Lord's Supper is to be found in the practice followed by Knox at Berwick, inasmuch as he substituted common bread for the bread wafers, and gave the first example of substituting sitting instead of kneeling in the receiving of communion.

At the close of 1550, Knox was transferred to Newcastle, where he remained until 1553. In 1551, he was appointed as one of the six chaplains to Edward the VI, and as such was consulted in the revision and sanction of The Articles concerning an Uniformity in Religion. Upon revision, these became the Thirty-nine Articles of the Church of England. Knox's last year in England was spent in London and the southern counties. As the royal chaplain, he preached in the court, and pleased King Edward, but twice was summoned to the privy council. Once to answer a complaint lodged by the duke of Northumberland, and once for denigrating the manner of observing Halloween.

About this time, the Duke of Northumberland proposed that Knox be made bishop of Rochester. This was the greatest test of character which he faced in his life. He stood in danger of corruption. We know this from a letter which Northumberland wrote to Cecil, Secretary of State, describing his reasons for offering Knox a bishopric, which was to use him for his own political purposes, and to control Knox (removing him from his pastorate in Newcastle and placing him within the Anglican hierarchy), thus bringing Knox into Anglican conformity. A later letter from Northumberland shows that Knox refused the bishopric, expressing his wish to return to his congregation in Newcastle and Berwick (largely Scot congregations near the border). The letter also suggests that Knox criticized Northumberland for his vices and covetousness.

Knox left for the north, and on Christmas day 1552 in Newcastle, preached a most daring sermon. He had learned from the court that King Edward was dying, and realizing that the Catholic Mary Tudor might soon come to the throne, he warned in his sermon the dangers of Papist rule looming ahead, a warning that might easily have cost him his head. It is significant that the only preacher in England who gave this warning was the Scottish immigrant, John Knox. Edward VI died in July 1553. After a nine-day reign, Lady Jane (grand-daughter of King Henry VIII and next Protestant in line for the throne) was deposed and later beheaded by her successor, Mary Tudor (Mary I of England and later called Bloody Mary), daughter of King Henry VIII by his first wife Catherine.

Mary, like her mother was Catholic in faith and in sentiment, and bore deep resentment towards her father and Protestants for the humiliation of her mother and herself during the divorce days. When she tried to reintroduce Catholicism to the realm she met with resistance, and soon a reign of terror ensued. Knox, who was outspoken in his opposition to Mary's appointment as queen, was persuaded to withdraw from England, and sailed for Dieppe (a port city in northern France), arriving in January 1554. The time afforded in his exile gave the refugee an opportunity of completing and publishing several treatises, a letter to his former congregations entitled: A Godly Letter of Warning or Admonition to the Faithful in London, Newcastle, and Berwick, general letters of encouragement to all the protestants in England entitled: Two Comfortable Epistles to his afflicted Brethren in England, and a letter to the Protestant ministers in England entitled: A Faithful Admonition to the Professors of God's Truth in England, all written in 1554. He lived for a season in Geneva, Switzerland in the congregation of John Calvin, and was most impressed. He accepted, in accordance with Calvin's council, an invitation to pastor an English congregation-in-exile at Frankfort. Soon after his arrival controversies arose in the congregation in regard to the use of the surplice (long white linen vestment worn by priests and Anglican ministers), the use or omission of the litany, and the kneeling at the receiving of communion (a practice described in the English Book of Prayer, but long opposed by Knox when he was in England). Knox showed amazing restraint and an uncharacteristic willingness to compromise, to preserve unity. An adversary in the congregation, desiring a strict adherence to the English Book of Prayer and seeking his position as pastor, forced him to resign by informing the magistrates of Frankfort (who were Protestant, but under the protection of the emperor) that Knox had used treasonable language in speaking of the emperor (Charles ?), the queen of England, and her husband Philip II. On March 26, 1555, John Knox resigned the pastorate and returned to Geneva, where he was asked to pastor a refugee English congregation, a considerable number of whom were supporters from the Frankfort congregation. Many historians cite this as the birth of English puritanism.

In August 1555, he visited Scotland preaching Evangelical doctrine in various parts of the country and persuading those who favored the Reformation to cease from attendance at mass, and to join with himself in the celebration of the Lord's Supper according to Reformed ritual. His practice was to meet secretly in private homes for communion in the various towns and cities where he preached. In May 1556, he was cited to appear before the ecclesiastical hierarchy in Edinburgh, and he boldly responded to the summons, but the bishops found it expedient not to proceed with the trial. Sometime during this visit to Scotland, Knox was married to Marjorie Bowes, daughter of Richard Bowes, captain of Norham Castle (we're not sure of the date, because John Knox never mentions it in his autobiographical History of the Reformation in Scotland). They were betrothed in 1553 before he left England. In July, an urgent call from his congregation at Geneva, along with the desire to prevent the renewal of persecution in Scotland, caused him to resume his Genevan ministry.

Knox's life in Geneva was no idle one. In addition to preaching and pastoral ministry, he carried on a great deal of significant correspondence with individuals in England and Scotland, and was constantly engaged in literary work. The literary works of that period, in addition to ten Familiar Epistles, include Letters to his Brethren and the Lord's, Professing the Truth in Scotland, An Apology for the Protestants who are Holded in Prison at Paris, The Appellation from the Sentence Pronounced by the Bishops and Clergy, A Letter Addressed to the Commonality of Scotland, An Epistle to the Inhabitants in Newcastle and Berwick, and A Brief Exhortation to England for the Speedy Embracing of the Gospel.

Judged by the excitement it created, the most outstanding writing of this period is The First Blast of the Trumpet Against the Monstrous Regiment of Women which he originally released anonymously. It was pointed against the two Catholic queens, Mary of Lorraine, regent Queen of Scotland, and "bloody Mary" queen of England, but John Knox had no way of knowing that the queen of England had very recently died (1558), and that her step-sister, Elizabeth, a staunch Protestant, succeeded her. It cannot be denied that this publication was untimely, and might be expected to expose the author to the resentment of two queens during whose reign it was his lot to live. He himself in retrospect seemed to realize that the First Blast was, in his words, "blown out of season," for although his original purpose was "thrice to blow the trumpet in the same matter, if God so permit," and on the last occasion to reveal his name, the intention was never carried into effect.

The resentment to which his blast against feminine government gave rise did not soon subside. One immediate effect was that, later, when Knox resolved to return to Scotland and wanted to pass through England, permission was denied. He continued to officiate in Geneva till January 1559, when he went home to Scotland to stay.

He arrived in Edinburgh on May 2, 1559, at a very critical time in Scottish history. During his absence the reform party had become more numerous, more self-reliant and aggressive, and better organized, The queen dowager, Mary of Lorraine, acting as regent for her daughter, the young Mary, queen of Scots, then in France, had become more desirous to crush the Protestants and determined to use force. Civil war was imminent, but each side shrank from the first step, Knox at once became the leader of the reformers. He preached against the "idolatry" of Catholicism, particularly the Mass, with the greatest boldness, and with the result that what he calls the "rascal multitude" began the "purging" of churches and the destruction of monasteries, destroying images and statuary, as well as looting. Knox did not approve of this action, but he never spoke out against it, as Martin Luther did when his followers engaged in vandalism, because he saw it as a force which would promote the overthrowing of an idolatrous religion.

Politics and religion were closely intertwined; the reformers were struggling to keep Scotland free from the yoke of France, and did not hesitate to seek the help of England. Knox negotiated with the English government to secure its support, and, in October 1559, he approved of the lords of his party suspending their allegiance to the regent queen. The death of the regent Queen Mary in June 1560 opened the way to a cessation of hostilities and an agreement leaving the settlement of ecclesiastical question to the Scottish estates, rather than the throne. John Knox and the party of Reformers, called the Congregation, drew up a petition proposing the abolition of Popish doctrine, the restoration of purity of worship and discipline, and the appropriating of ecclesiastical revenues to the support of the ministry, the promotion of education, and the relief of the poor. This document, called The Confession of Faith Professed and Believed by the Protestants within the Realm of Scotland (The Confession), was presented to the Scottish parliament and was ratified on August 17, 1560. The doctrine, worship and government of the Roman Church were overthrown and Protestantism was established as the national religion (The Confession remained the authorized Scottish creed for two centuries). Soon afterwards, John Knox and three other ministers drew up the plan of ecclesiastical government, known as the First Book of Discipline. This standard document, approved by the General Assembly and subscribed by a majority of the members of privy council, is incorporated in Knox's History, along with The Confession.

Mary, queen of Scots, youthful, widowed, and fair, arrived in Scotland in August 1561, thoroughly predisposed against Knox, while he and the other Reformers looked upon her with grave suspicion, both as a foreigner and as an adamant Papist with designs of re-establishing Catholicism in the realm. She swore to uphold the laws of the land, and to forbid the practice of the Mass anywhere within the realm, but was permitted to attend her own private Mass in the palace chapel. John Knox was very much against even that, seeing in it a first step for Scotland on the road back to papism. She lost no time in summoning Knox to the palace of Holyrood, to hold with him the first of five personal interviews. He found her no mean opponent in argument, and had to acknowledge the acuteness of her mind, if he could not commend the qualities of her heart. His attitude from the very beginning was unyielding and repelling, abrupt, and confrontational, his language and manner harsh and uncourtier-like, perhaps acceptable behavior for a Whitehouse news correspondent today, but considered rude and disrespectful to a queen in those times. It must be remembered that the momentous issues at stake required a plain-spoken prophet like John the Baptist, not a smooth-tongued statesman. Nonetheless, it might have been wiser at the outset of their intercourse, to seek to win rather than repel.

When the Reformed religion was formally ratified by law in Scotland in 1560, Knox was appointed minister of the Church of St. Giles, then the great parish church of Edinburgh. He was at this time in the fullness of his powers, as is manifest abundantly in the style of History of the Reformation- a work which appears to have been begun about 1559 and completed in the course of the next six or seven years. Knox was truly a great man, compassionate in his regard for the poor, as a shepherd of souls a man fervent and considerate, pure in his personal life, loyal in friendship, untainted by jealousy, genial and amiable in private character. In his History, however, we see his public and political life, which was much less admirable. It cannot be relied upon as an entirely objective historical account. His favorite adjectives are "bloody," "beastly," "rotten," and "stinking," expressing bitterness and vindictiveness. If sometimes rough and even course language, and not always commendable in temper and spirit, it is written with a force and vigor not surpassed by any of his other writings, truly a work of genius. At the very beginning of his labors as minister of Edinburgh, his wife died, leaving two sons, Nathanael, who died at Cambridge in 1580, and Eleazer, who became vicar of Clacton Magna and died in 1591.

Queen Mary, after various failed attempts to win John Knox's favor through flattery and tears, endeavored to get him into her power by moving the privy council to pronounce him guilty of treason based on a circular letter he had written to leading Protestants regarding the trial of two persons indicted for a riot in the Chapel Royal. Knox's trial took place at a special meeting of council in December 1562, at which the Queen was present and acted in the unseemly role of prosecutrix. To her chagrin, and extreme displeasure, Knox was acquitted and absolved from all blame by a majority of the noblemen present, and commended for his judicious defense.

In June 4, 1564, there was a debate at the General Assembly of the Parliament between the Protestant lords and courtiers on the one hand, and the leading superintendents and preachers. Most of the debating was done by Lord Lethington representing the nobles, and Knox representing the preachers. Lethington began by objecting to the fact that Knox, in his sermons, called Mary a slave of Satan, which stirred up the people against the Queen and her servants. Knox replied that Mary was a rebel against God, because she maintained that idol, the mass. When Lethington said that Mary was sincerely convinced that her mass was good religion, Knox said that the men who had offered their children to Molech were also convinced that their religion was right, but in fact they were rebels against God. Lethington challenged Knox's doctrine that the people are punished for the sins of their rulers, and will only be saved if they resist their wicked princes. "Then will ye make subjects to control their princes and rulers?," asked Lethington. Knox replied, "And what harm should the commonwealth receive, if that the corrupt affections of ignorant rulers were moderated, bridled by the wisdom and discretion of godly subjects." Lethington admitted that the Bible orders that the idolater shall die the death, but "there be no commandment given to the people to punish their king if he was an idolater." Knox answered, "I find no more privilege granted unto kings than unto the people, to offend God's majesty."

They argued at length on all the examples from the Old Testament, especially the account in 2Kings 9 and 10 of Jehu, who assassinated King Ahab and his entire family in obedience to divine command. Lethington claimed that Jehu was already a king when he killed Jezebel, having been anointed by the prophet. Knox insisted that Jehu was a mere subject, prophesied to be king, but not yet recognized as king, indeed thought to be a traitor by Jezebel. At one point Lethington asked Knox, "how are ye able to prove that ever God struck or plagued a nation or people for the iniquity of their prince, if they themselves lived godly?" Knox replied, "The Scripture of God teaches me that Jerusalem and Judah was punished for the sin of Manasseh, and if ye will claim that they were punished because they were wicked and offended along with their King, I answer that the text says, 'Manasseh made Judah and the inhabitants of Jerusalem to err.' True it is, for though people willingly followed him in his idolatry, the king, by reason of his authority, led the people in defiling all Jerusalem and the temple of God with all abominations, and so were they all criminal for their sin; the one by act and deed, the other by suffering and permission: even as all Scotland is guilty this day of the Queen's idolatry, and ye my Lords, specially above all others."

When it came to citing the opinions of the leading thinkers of the age, Knox could not compete with Lethington, for he did not have the support of tradition or the reformers. Lethington cited Luther, Melanchthon, Bucer, and Calvin in his support. All of these men would agree that it is proper for a Christian to refuse to obey civil authority when it contradicts God's law (passive civil disobedience), but that it is not proper for a Christian to take up arms and overthrow that authority (revolution) for the same reason. Against them, Knox could only quote the Apology of Magdeburg, issued by the Protestant ministers of the city when they rose to resist the Emperor Charles V in 1550, which he summarized in one sentence: "That to resist a tyrant is not to resist God, nor yet His ordinance." In this discussion the participants seem to stand on the threshold that separates the medieval from the modern world, the worldly young statesman standing for the old, the aging preacher standing for the new. The opinion of the day may have been against Knox, but the future was on Knox's side.

During this time, March 1564, John Knox married his second wife, Margaret Stewart of Ochiltre, daughter of Lord Ochiltre. Knox was 50 and Margaret was 17. Marriages between elderly men and young girls were not at all uncommon in the sixteenth century, but Calvin had condemned them as undesirable, and had criticized Farel when at the age of 69, he married a girl who was under 16. What made the marriage more controversial for some was the fact that Knox was a man of humble birth, whereas Margaret was the daughter of a duke and in fact of royal blood. It was reported that Queen Mary "stormeth wonderfully," which would read today, "had a temper tantrum," when she heard about the marriage, "for that she is of the blood and name". The only way that the Catholics could explain the fact that Knox had been accepted by Lord Ochiltre and Margaret was that he "resorted to witchcraft."

In July of 1565, Mary married a handsome, unscrupulous 18 year old Catholic Scottish nobleman named Lord Darnley, from the Stuart family, that claimed to have the right of heir to the throne in Scotland if Mary should die childless. Up until this time, the Protestant lords had the support of Mary, and many felt that this support would be lost with this marriage. One Protestant lord named Moray, Mary's half-brother and one of her principal advisers, realizing that this meant the end of his influence at Court, was assembling the Protestant lords and preparing for armed insurrection. Mary and Darnley, not wanting the armed conflict to take the form of a religious war, issued a proclamation in which they declared their intention of preserving the Protestant religion, and reissued Mary's proclamation of 1561, prohibiting anyone, on pain of death, from attempting to alter the state of the Protestant religion that existed in Scotland when the Queen first returned from France. In line with this policy of appeasement, Lord Darnley attended John Knox's service at St. Gile's on Sunday, August 19, 1565. As he listened to the sermon, Lord Darnley was enraged by what he perceived were references to himself and his queen as King Ahab and Jezebel. He returned to the palace with the determination not to taste food till the offender had been punished. Knox was called to appear before the privy council, "from my bed" as he recalls. Informed that he had offended the king and that he must desist from preaching as long as their majesties remained in Edinburgh. Knox replied that he had spoken nothing but according to his text (Is 26:13-21), and if the church should command him either to speak or abstain, he would obey, so far as the word of God would permit him. In regard to the sermon, he deemed it necessary for his own exoneration to write it out in full what he had spoken and publish it with a preface. This is the only sermon of John Knox which has been preserved.

On September 1, 1565, Moray and some of the other rebel Protestant lords, not the majority but a small faction, took control of Edinburgh, but 34 hours later were driven from the city. The royal army chased them in circles all over Scotland, until the rebels crossed the frontier into England. Queen Elizabeth refused to extradite them, but rebuked them sorely for having dared to resist their queen. It was a hard time for Scotland. Due to two exceedingly harsh winters in succession, starvation was rampant. Protestant ministers, deprived of the stipend that the Catholic clergy had enjoyed, had to rely on their congregations, many of whom were too poor to support them. Mary denied the request of the General Assembly to surrender her half of "the thirds" for the support of the clergy. Knox wrote a letter of encouragement to all the ministers, urging them not to give up their vocation, and another to the brethren of the Congregation, to support their own ministers, who were resigning for lack of food. The General Assembly declared a fast, and Knox wrote a document explaining reasons for the fast: the brethren had allowed the return of the Catholic mass to the realm (not mentioned was the humiliating defeat of the Protestant rebels); the nobility and the wealthy class were oppressing the poor; and on the mainland, the Catholics had declared war on the Protestants at the Council of Trent, with plans to systematically exterminate Calvinists and Lutherans. Already 100,000 Huguenots had been slaughtered in France.

At the end of February 1566, Mary expelled more Protestant lords from Scotland when she discovered they were supporting Moray. On March 7, she opened Parliament with the intention that they should pass an Act that would declare all those who fled to England as traitors, and their property be confiscated. There were rumors that she was planning to join a Catholic league, with the Pope, the Emperor, the King of Spain, and others. Twelve wooden altars, to be erected in St. Giles, are said to have been found in Holyrood. Two days later, on the evening of March 9, 1566, a band of some twenty men broke into the Queen's room in the palace at Holyroodhouse, and murdered her secretary David Riccio, dragging him from the dining room where he was having supper with the Queen and a few others, stabbing him to death in the ante-room, and holding the Queen prisoner in the palace. The leader of this mob was, guess who, the Queen's husband, the King (Lord Darnley had convinced Mary to give him the title of King but now he was interested in securing the Crown). Apparently, certain of the Protestant lords plotted with the King to murder Riccio after preying on the his jealousy and suspicion that Riccio was an adulterer who had seduced the Queen. They promised him that they would persuade Parliament to grant him the Crown along with his title of King. After murdering Riccio, the murderers held the queen prisoner in the palace. On the same night, one of the Queen's Catholic friars was murdered in his bed.

The next day a proclamation was given in the King's name, disbanding the meeting of Parliament, and that evening Moray and company returned from England to Edinburgh. Knox does not relate the story in his History, which ends its chronology in June 1564. But he does allude to the incident in the first Book of the History, with these regrettable words; "in plain terms let the world understand what we mean, that great abuser of this commonwealth, that vile knave Davie (Riccio) was justly punished, the ninth of March, in the year of God 1565... by the hands of James Douglas, Patrick Lord Lyndesay, Lord Ruthven, with others in their company, who all, for their just act, and most worthy of all praise, are now most unworthely left of their brethren, and suffer the bitterness of banishment and exile." For John Knox to call this treacherous act of murder a "just act, most worthy of praise" shows how far, in his political intrigueing, he had strayed from his Christian ideals as a young man. The murder of Riccio was far more reprehensible than the murder of Cardinal Beaton. Riccio was not killed because he was a persecutor on whom the Protestants were inflicting retribution, or even because he was a formidable enemy of the cause, but merely for the politically beneficial consequences which would result from the Queen's secretary being murdered by the Queen's husband. If Riccio was indeed guilty of adultery, the nobles might easily have taken, tried, and hanged Riccio.

Two days later after the murder of Riccio, Mary persuaded Darnley to desert his confederates and help her to escape to Dunbar. There they raised an army, and prepared to advance against Edinburg. When news of this reached Edinburg, all the participants in the coup fled the city. Whether he knew beforehand about the plot or not, his running away did not disarm suspicion. Knox left town the same day, "with a great mourning of the godly of religion" says a diarist. The night before leaving, he composed a soul-searching and melancholic prayer, wherein he asks God to take his life (Knox 6, 483). The killers of Riccio fled to England. Moray and the rebels were pardoned by Mary, but the killers of Riccio had taken their places in exile, taking refuge in England. Knox was not associated with the murderers and was allowed to return to Edinburg. That Christmas Eve, Mary pardoned all the murderers of Riccio. Knox received permission to visit his sons in Northumberland, England who were under the care of his mother-in-law from his first marriage, Mrs. Bowes. He carried with him a letter from the Congregation against the treatment of Puritans who had conscientious objections to the apparel of the Anglican church.

While Knox was away in England, a lot happened. The Queen had a baby, James (James VI, King of Scotland and later, James I, King of England), who was baptized a Catholic. Her husband Lord Darnley was murdered. The Queen then married the man who murdered her husband, a protestant nobleman by the name of Bothwell, with whom she had been having an affair prior to the murder, and more than likely with whom she plotted the murder of her husband. Mary sought to befriend the Protestants by being married to her new husband by the Protestant bishop of Orkney and by granting a large subsidy for the support of Protestant ministers. However, she alienated the Catholic Church without gaining the support of the Protestants, who saw her as an adulteress and an accomplice in murder. She was arrested and imprisoned, her infant son was crowned King, and Moray, a Protestant, was named regent. Knox called for the execution of Mary. However, Mary managed to escape, rallied her supporters, and a civil war ensued between those who supported Mary as Queen, mostly Catholics but some Protestants, and those who supported the infant King and Moray. Her army was defeated by regent Moray on May 12, 1568. Four day later, Mary fled to England and sought the refuge of Queen Elizabeth.

Knox's life was drawing to a close in a very dark chapter in Scottish history. Moray was assassinated, and two of the three successive regents were also assassinated. He had one thing to be very happy about: when Mary sought refuge in England, Queen Elizabeth made Mary a prisoner for the rest of her life. In 1586, after many plots and attempted escapes, Mary was exposed in a hare-brained plot to assassinate Queen Elizabeth and gain the crown of both England and Scotland. Mary was tried, sentenced to death, and then beheaded in February 1587.

When Knox was dying he asked his wife to read aloud the seventeenth chapter of John's gospel, saying "Go read where I cast my first anchor," referring to many years ago, when, as a poor Catholic cleric, he first trusted in Christ. He died November 24, 1572.