After this, several skirmishes ensued between the queen and lords of the congregation. But at last, the queen sickened and died, and a general peace, which lasted for some time, was procured, during which, the commissioners of the Scots nobility (anno 1560), were employed in settling minsters in different places. Mr. Knox was appointed to Edinburgh, where he continued until the day of his death.
The same year the Scots confession was compiled and agreed upon; and that the church might be established upon a good foundation, a commission and charge was given to Mr. Knox and five others, to draw up a form of government and discipline of the church. When they had finished it, they presented it to the nobility, by whom it was afterwards ratified and approved of.
But this progress which was daily making in the reformation, soon met with a severe check by the arrival of queen Mary from France in August 1561.; with her came popery and all manner of profanity; the mass was again publicly set up, at which the religious part of the nation were highly offended, and none more than Mr. Knox, who ceased not to expose the evil and danger of it on every occasion: On which account the queen and court were much exasperated. They called him before them, and charged him as guilty of high treason. The queen being present, produced a letter, wrote by him, wherein it was alledged that he had convocated her majesty's lieges against law; whereupon a long reasoning ensued between him and secretary Lethington upon the contents of said letter; in which Mr. Knox gave such solid and bold answers, in defence of himself and doctrine, that at last he was acquitted by the lords of the council, to the no small displeasure of the queen and those of the popish party.
Mr. Knox, in a conference with the queen about this time, said, "If princes exceed their bounds, they may be resisted even by power, for there is no greater honour and obedience to be paid to princes than God hath commanded to be given to father and mother. If children join together against their father stricken with a frenzy, and seeking to slay his own children, apprehend him, take his sword or other weapons from him, bind his hands, and put him in prison till his frenzy overpass, do they any wrong, or will God be offended with them for hindering their father from committing horrible murder?—Even so, madam, if princes will murder the children of God their subjects, their blind zeal is but a mad frenzy. To take the sword from them, to bind them, and to cast them into prison till they be brought to a sober mind, is not disobedience, but just obedience, because it agreeeth with the word of God." The queen hearing this, stood for some time as one amazed, and changed countenance. No appearance was, at this time, of her imprisonment[33].
After the queen's marriage with Henry earl of Darnly, a proclamation was made in 1565, signifying, That forasmuch as certain rebels who, under the colour of religion, (meaning those who opposed the measures of the court) intended nothing but the subversion of the commonwealth, therefore they charged all manner of men, under pain of life, lands, and goods, to resort and meet their majesties at Linlithgow on the 24th of August. Upon Sabbath the 19th, the king came to the high church of Edinburgh, where Mr. Knox preached from these words, O Lord our Lord, other lords, beside thee, have had the dominion over us, &c. In his sermon he took occasion to speak of wicked princes, who, for the sins of a people, were sent as scourges upon them, and also said, "That God set in that room boys and women; and that God justly punished Ahab and his posterity, because he would not take order with the harlot Jezebel." These things enraged the king to a very high degree. Mr. Knox was immediately ordered before the council, who went thither attended by some of the most respectable citizens; when called in, the secretary signified that the king was much offended with some words in his sermons, (as above-mentioned), and ordered him to abstain from preaching for fifteen or twenty days; to which Mr. Knox answered, That he had spoken nothing but according to his text, and if the church would command him either to speak or refrain from speaking, he would obey so far as the word of God would permit him. Nevertheless, for this and another sermon which he preached before the lords, in which he shewed the bad consequences that would follow upon the queen's being married to a papist, he must be, by the queen's order, prohibited from preaching for a considerable time.
It cannot be expected, that we should enumerate all the indefatigable labours, and pertinent speeches which, on sundry occasions, he made to the queen, nor the opposition which he met with in promoting the work of reformation; these will be found at large in the histories of these times.
The popish faction now found, that it would be impossible to get their idolatry re-established, while the reformation was making such progress, and while Mr. Knox and his associates had such credit with the people.—They therefore set other engines to work, than these they had hitherto used; they spared no pains to blast his reputation by malicious calumnies, and even by making attempts upon his life; for, one night as he was sitting at the head of a table in his own house, with his back to the window, (as was his custom), he was fired at from the other side of the street, on purpose to kill him; the shot entered at the window, but he being near to the other side of the table, the assassin missed his mark; the bullet struck the candlestick before him, and made a hole in the foot of it: Thus was he that was with him, stronger than they that were against him.
Mr. Knox was an eminent wrestler with God in prayer, and like a prince prevailed; the queen regent herself gave him this testimony, when, upon a particular occasion, she said, She was more afraid of his prayers than of an army of ten thousand men. He was likewise warm and pathetic in his preaching, in which such prophetical expressions as dropt from him, had the most remarkable accomplishment; as an instance of this, when he was confined in the castle of St. Andrews, he foretold both the manner of their surrender, and their deliverance from the French gallies; and when the lords of the congregation were twice discomfited by the French army, he assured them, in the mean time, that the Lord would prosper the work of reformation. Again, when queen Mary refused to come and hear sermon, he bid them tell her, That she would yet be obliged to hear the word of God whether she would or not; which came to pass at her arraignment in England. At another time he thus addressed himself to her husband Henry, lord Darnly, while in the king's seat in the high church of Edinburgh, "Have you for the pleasure of that dainty dame cast the psalm book in the fire; the Lord shall strike both head and tail;" both king and queen died violent deaths. He likewise said, when the castle of Edinburgh held out for the queen against the regent, that "the castle should spue out the captain (meaning the laird of Grange) with shame, and that he should not come out at the gate, but over the wall, and that the tower called Davies tower should run like a sand-glass;" which was fulfilled in a few years after, the same captain being obliged to come over the wall on a ladder, with a staff in his hand, and the said forework of the castle running down like a sand brae.
On the 24th of January 1570, Mr. Knox being in the pulpit, a paper was put into his hands among others, containing the names of the sick people to be prayed for; the paper contained these words, "Take up the man whom you accounted another God," (this alluded to the earl of Moray who was slain the day before). Having read it he put it in his pocket, without shewing the least discomposure. After sermon, he lamented the loss which both church and state had met with in the death of that worthy nobleman, (meaning the regent) shewing, that God takes away good and wise rulers from a people in his wrath, and, at last, said, "There is one in the company who maketh that horrible murder, at which all good men have occasion to be sorrowful, the subject of his mirth; I tell him, he shall die in a strange land, where he shall not have a friend near him to hold up his head," One Mr. Thomas Maitland being the author of that insulting speech, and hearing what Mr. Knox said, confessed the whole to his sister the lady Trabrown, but said, That John Knox was raving to speak of he knew not whom; she replied with tears, That none of Mr. Knox's threatenings fell to the ground. This gentleman afterwards went abroad, and died in Italy, on his way to Rome, having no man to assist him.
Mr. Knox's popularity was now so well established, that the malignant party, finding it impossible to alienate the hearts of the people from him, began now openly to work his destruction, fortifying the town and castle with their garrisons; they vented their malice against him by many furious threatenings. Upon which he was urged by his friends to leave Edinburgh for his own safety, which at last he did in May 1571, and went to St. Andrews, where the earl of Morton (who was then regent), urged him to inaugurate the arch-bishop of that see. This he declined, with solemn protestations against it, and denounced an anathema on the giver and receiver. Though he was then very weak in body, he would not refrain from preaching, and was obliged to be supported by his servant Richard Bannantyne, in going to church; and, when in the pulpit, he behoved to rest sometime before he could proceed to preach, but before he ended his sermon, he became so vigorous and active, that he was like to have broken the pulpit to pieces.