At this juncture, Mr Knox landed in Scotland from France, and, after residing two days in Edinburgh, joined his brethren in Perth, that he might aid them in their cause, and give his confession along with theirs. On the 11th, the day after the sentence of outlawry was pronounced, he made a vehement discourse against idolatry, and while the minds of the people were yet in a state of agitation, from the impression made upon them by his sermon, a priest prepared to celebrate mass, which made a youth observe, “This is intolerable, that when God in his word hath plainly condemned idolatry we shall stand and see it used in despite.” The irritated priest struck him a blow on the ear, and the youth in revenge threw a stone at him, which broke an image of one of the saints. This was the signal of tumult, and ere two days had elapsed, all the churches and convents about Perth were destroyed. Such was the anger of the Queen on receiving this intelligence, that she avowed to reduce Perth to ashes, and ordered M. D’Ossal, the commander of a corps of French auxiliaries, at that time in the service of Scotland, instantly to march, and carry her threats into execution. Both parties, however, were desirous of accommodation, and a treaty was concluded, in which it was stipulated that the two armies should be disbanded, the gates of Perth set open to the queen, but that none of her French soldiers should approach within three miles of that city, and that a Parliament should be immediately held to settle the remaining differences.

No sooner were the Protestant forces disbanded, than the Queen violated every article of the treaty. In consequence of which the earl of Argyle, and the prior of St Andrew’s, who had been her commissioners for settling the peace, with some other gentlemen, openly left her. Having warned the confederates of her intention to destroy St Andrew’s and Cupar, a considerable army was soon assembled, which assaulted Crail, broke down the altars and images, and proceeded thence to St Andrew’s, where they levelled the Franciscan and Dominican monasteries to the ground. The Queen immediately gave orders to occupy Cupar, with the intention of attacking them at St Andrew’s, but in this she was anticipated, an army equal to her own having occupied the place two days before. Finding herself too weak to encounter them in the field, she had again recourse to negotiation; but mindful of her former duplicity, the Protestants would only agree to a truce for eight days, by which the Duke of Chatelherault and D’Ossal became bound to transport all the French soldiers to the other side of the Frith, and send commissioners to St Andrew’s with full powers to conclude a formal treaty of peace.

Several days elapsed without any person appearing on the part of the queen, and suspecting some new plan to entrap them, the Protestants, after concerting measures to expel the French garrison from Perth, wrote to her Majesty, complaining that the terms of the first treaty were still unfulfilled, and begging her to withdraw her troops from that city in conformity with its stipulations. Their letters remaining unnoticed, they laid siege to Perth, which surrendered, after a feeble resistance, on the 26th June, 1559.

Being informed that the Queen resolved to seize Stirling, and cut off the communication between the reformers on the opposite sides of the Frith, by a rapid march they frustrated her plans, and in three days, after they had made themselves masters of Perth, the victorious reformers entered Edinburgh. The Queen on their approach retired to Dunbar,—where she amused them with hopes of an accommodation, in the expectation of being joined with reinforcements from France. Intelligence, in the meantime, was received of the death of the French king, which, while it was favourable to the cause of the reformers, rendered their leaders more negligent and secure. Numbers of them left the city on their private affairs, their followers were obliged to disperse for want of money, and those who did remain were without discipline or restraint. The Queen receiving advice of this, by means of her spies, marched with all the forces she could muster directly to Edinburgh, and possessed herself, on the 25th of July, of Leith. She consented, however, to a truce, to continue till the 5th January, 1560, by which liberty of conscience was secured; Popery was not to be established again where it had been suppressed, the reformers were not to be hindered from preaching wherever they might happen to be, and no garrison was to be stationed within the city. These terms were preserved till she received the expected reinforcements, when she fortified Leith, from which all the efforts of the reformers were unable to dislodge her troops. A mutiny also breaking out among their soldiers for want of pay, and having been defeated in two skirmishes with the French troops, it was resolved, by a majority of the lords of the congregation, to retire to Stirling. This rash step was productive of great terror and confusion, and contrary to the advice of Knox; who, notwithstanding, followed the fortunes of his friends, animating and reviving them by his discourses, and exhorting them to constancy in the good cause.

At a meeting held shortly after their arrival at Stirling, it was resolved, to despatch William Maitland, who had lately deserted the Queen’s party to England, to implore the assistance of Queen Elizabeth, and a treaty was at last concluded, by which a body of troops was sent to their assistance. These being joined by most of the Scottish nobility, a peace was established on the 8th July, 1560, by which the reformed religion was fully established in Scotland.

On the abolition of Popery, the form of church goverment establishment in Scotland was, upon the model of the church at Geneva, warmly recommended to his countrymen by Knox, as being farthest removed from all similarity to the Romish church; and at his suggestion, likewise, the country was divided into twelve districts, for the more effectually propagating the doctrines of the Reformation, of which Edinburgh was assigned to his care. Knox, assisted by his brethren afterwards composed a confession of Faith, and compiled the first books of discipline for the government of the church. These were ratified by a convention of Estates, held in the beginning of the following year (1571), and an act passed prohibiting mass and abolishing the authority of the Pope.

On the return of Mary, daughter of Mary of Guise, from France, and so well known afterwards throughout all Europe for her beauty, her accomplishments, and her misfortunes, after the death of her husband Francis II. the celebration of mass in the chapel royal excited a great tumult, many crying out, “The idolatrous papist shall die the death, according to God’s law;” and John Knox, in a sermon preached the Sunday following after showing the judgments inflicted on nations for idolatry, added, “one mass is more fearful to me than if ten thousand armed enemies were landed in any part of the realm, of purpose to suppress the whole religion.” In consequence of this language he was sent for by the queen, who accused him of endeavouring to excite her subjects to rebellion, of having written against her lawful authority, and of being the cause of great sedition. To this he answered, among other things, “that if to teach the word of God in sincerity, if to rebute idolatry, and to will a people to worship God according to his word, be to raise subjects against their princes, then cannot I be excused; for it hath pleased God in his mercy to make me one amongst many to disclose unto this realm the vanity of the papistical religion.—And touching that book, that seemeth so highly to offend your majesty, it is most certain that if I wrote it I am content that all the learned of the land should judge of it. My hope is, that, so long as ye defile not your hands with the blood of the saints of God, that neither I nor that book shall either hurt you or your authority; for, in very deed, Madam, that book was written most especially against that wicked Mary of England.” To a question by the Queen, if subjects, having power, may resist their princes? He boldly answered they might, “if princes do exceed their bounds.” The following part of the dialogue will give a good idea of the character of Knox, and the freedom of his speech: Speaking of the church, the Queen observed, “but ye are not the church of Rome, for I think it is the true church of God.” “Your will, Madam,” said he, “is no reason; neither doth your thought make that Roman harlot to be the immaculate spouse of Jesus Christ. And wonder not, Madam, that I call Rome an harlot, for that church is altogether polluted with all kinds of spiritual fornication, as well in doctrine as in matters.” He had afterwards two other conferences with the queen, at the last of which she burst into tears, crying out, “Never prince was used as I am.”

Knox’s situation became very critical in April, 1571, when Kircaldy received the Hamiltons, with their forces, into the castle. Their inveteracy against him was so great, that his friends were obliged to watch his house during the night. They proposed forming a guard for the protection of his person when he went abroad; but the governor of the castle forbade this, as implying a suspicion of him, and offered to send Melvil, one of his officers, to conduct him to and from church. “He wold gif the woulf the wedder to keip,” says Bannatyne. Induced by the importunity of the citizens, Kircaldy applied to the Duke and his party for a special protection to Knox; but they refused to pledge their word for his safety, because “there were many rascals and others among them who loved him not, that might do him harm without their knowledge.” Intimations were often given him of threatenings against his life; and one evening, a musket ball was fired in at his window, and lodged in the roof of the apartment in which he was sitting. It happened that he sat at the time in a different part of the room from that in which he had been accustomed to take his seat, otherwise the ball, from its direction, must have struck him. Alarmed by these circumstances, a deputation of the citizens, accompanied by his colleague, waited upon him, and renewed a request which they had formerly made, that he would remove from Edinburgh, to a place where his life would be in greater safety, until the Queen’s party should evacuate the town. But he refused to yield to them, apprehending that his enemies wished to intimidate him into flight, that they might carry on their designs more quietly, and then accuse him of cowardice. Being unable to persuade him by any other means, they at last had recourse to an argument which prevailed. Upon this he consented, “sore against his will,” to remove from the city.

In May, 1571, at the desire of his friends, and for greater security, he left that city for St Andrew’s, where he remained until the August following. The cause that forced him to change his residence having ceased to operate, at the express desire of his congregation he again returned, but could not long continue to preside over it, on account of the exhausted state of his health; and on the 9th November, abmitted Mr James Lawson, formerly professor of philosophy at Aberdeen, to be his successor.

From this time till the 24th of the same month, when he expired, about eleven o’clock at night, in the 67th year of his age; his principal employment was reading the Scriptures and conversing with his friends; and over his remains, which were accompanied to the churchyard by the Earl of Morton, the Regent, and a number of other noblemen, and people of all ranks, his lordship pronounced the following eulogium: “Here lies a man, who in his life never feared the face of man; who hath been often threatened with dag and dagger, but yet hath ended his days in peace and honour.”