After the death of Murray, for a short time it was doubtful what course Kirkaldy would pursue: once he had almost resolved to own the authority of the young king, fearing that, by remaining under a hostile flag, he might injure the cause of Mary while exiled; and he felt reluctance to embroil once more his native land in blood, for he had sincerely its honour and interest at heart.

Summoned by his foe Morton, he attended a meeting held in the city with the envoys of Elizabeth, Henry Gates and William Drury, knights; Wishart of Pitarrow, his constable, and Tullybardine his friend, accompanied him. What part he took in the proceedings does not appear ; but soon after, by Elizabeth’s influence, Lennox, the father of Darnley, was by a convention of the nobles declared regent of the realm during the minority of his grandson. Kirkaldy, whose mind was wholly bent on the restoration of Mary, by the castle guns could easily have laid in ruins the Tolbooth where the convention sat; but, treating the whole affair with supreme contempt, he refused to deliver up the regalia to officials sent for it— refused to be present, or to hear Elizabeth’s letter read by her ambassador, and issued orders tbat not a cannon-shot should be fired in honour of Lennox’s proclamation as regent.

So restless is the ambition of Morton said to have been, that, after Lennox was proclaimed, he went secretly in the night to the castle of Edinburgh, accompanied by Master Archibald Douglas, regardless of the unanswered gages of defiance hurled at them by Kirkaldy and Lord Herries. There Morton displayed his baseness, by craving their assistance to drive Lennox out of Scotland, and procure his own acknowledgment as regent instead. Amazed by his effrontery, Chatelherault and Kirkaldy peremptorily refused, and briefly dismissed the earl, who, baffled and enraged, had to smother his feelings and retire covered with shame. Meanwhile Lennox, a weak-minded noble, goaded by the memory of his son’s fate, proceeded to the utmost extremities with the adherents of Mary. The Duke of Chatelherault, the Earl of Huntly, Lord Herries, Sir William Kirkaldy, and all their followers, were denounced as traitors and enemies to their country. Factious and turbulent as Scotland had been previous to Murray’s death, the horizon of the future became darker, and a furious civil strife was anticipated by all. The party of Mary drew to a head at Linlithgow, and sent an order to Kirkaldy, by which he released a number of prisoners who had been committed to his charge for their opposition to Murray and King James. Maitland of Lethington, who had gone to Linlithgow, soon afterwards returned, and held a conference with Kirkaldy near St Cuthbert’s Kirk, arranging the mode of reception for the queen’s lords, should they move to the capital, which they did on the 13th April.1 Some time previous to this, the secretary had been, hy the king’s privy council, declared innocent of Damley’s murder, and of any participation in it.

The standard of Mary had replaced that of her son on the ramparts of the fortress, and the lords of her faction now possessed the capital. There is something pathetic in the manner of Bannatyne, in his additions to Knox’s “Historic,” when bewailing the defection of Kirkaldy.

"Alace! Sir William Kirkcaldie, sometyme stout and true lairde of Grange; miserable is thy fall, who now drawest in yoke with knawen and manifest traitouris— that sometyme had place amongst honest hearts, yea, among the saints of God—hut Judas joyed not long the price of innocent blood!”

Maitland arrived at Leith while labouring under a severe illness, and was borne to the castle on the shoulders of six soldiers. Soon afterwards Kirkaldy sent Captain Melville with a party to search the premises of Lickprevick a printer, and to destroy all copies of Buchanan’s Chamelion, a pamphlet in which the politics of the secretary were severely handled. A parliament was held in May 1571, by the queen’s party, who rode in procession to the palace and back again, with the regalia borne before them, and they passed and enacted laws which were doomed never to he put in force.

The king’s party taunted Kirkaldy with having been bribed to join Mary, by the promise of the rich priory of St Andrews. "Brother William,” said his old friend Randolph, the English ambassador, in a bantering letter addressed to him, 1st May 1570, “it was, indeed, most wonderful to me when I heard that you should become Prior. That vocation agreeth not with any thing that ever I knew in you, saving for your religious life led under the cardinal’s hat, when we were both students at Paris.

The arrival of Monsieur le Yerac, an envoy from the court of France, with letters of encouragement and ample promises of aid to Kirkaldy and other leaders, together with similar offers from the court of Madrid, infused new life into the queen’s faction. Le Yerac served to give a sudden check to the friends of Lennox; and the English envoy, the wily and intriguing Randolph, had to fly for refuge to his own frontier town of Berwick; while a general convention of the nobles was ordered to be held at Leith, for the avowed purpose of putting an end to the miserable dissensions which rent Scotland, arming man against man—brother against brother.

Elizabeth now became alarmed at the promises of aid which the loyalists received from foreign princes; she deceived them by appointing commissioners to meet those of Mary, in order to arrange matters for an ultimate restoration to her throne. But nothing could be farther from the mind of this subtle princess, whose only object was to tyrannise over a rival whom she equally hated and envied for her surpassing beauty, and whom her fierce subjects and unfortunate destiny had thrown so utterly at her mercy. She had another aim in view: by increasing the dissensions of so martial and turbulent a people as the Scots, she rendered her throne more secure.

Menaced as she was by rebellion at home and invasion from abroad, peace in Scotland would infallibly have rendered her authority unsteady; and the increased fury of the civil war, which always succeeded the pretended negotiations of her dishonourable envoys, evinces how well they understood and acted up to the fullest intentions of their mistress. In pursuance of her system, she desired the proposed commission for Mary’s restoration to be suddenly abandoned, and submitted the poor captive to a more rigorous captivity than ever.

Meanwhile the Scottish loyalists increased daily in number and in power. The Duke of Chatelherault, head of the Hamiltons, Argyle and nine other earls, Home and thirteen other lords—the representatives of the greatest and most noble families in Scotland—were avowedly in the faction, which must soon have triumphed, but for the paralysation caused by the underhand intrigues of Elizabeth and her ministry. They possessed the fortresses of Edinburgh, Dunbarton, and Lochmaben, three of the strongest in the kingdom: the first every way important, as commanding and overawing the capital ; the second, on the Clyde, affording a safe port for the expected foreign succours; and the third, an ancient castle on the frontiers in Annandale. Kirkaldy, with his brave and well-disciplined garrison, occupied the first, having as his constable Wishart of Pitarrow;1 John lord Fleming, a gallant soldier, had maintained the second for Mary at all hazards, since the beginning of the civil wars. But the chief strength of the faction lay in Sir William Kirkaldy and Maitland; the first being reputed the most fortunate soldier, and the second the most able statesman in Scotland. It was generally believed that, with two such heads to direct them, Mary’s party would soon be more than a match for their opponents.

Open war was soon proclaimed—a war to which Morton, a man bred up from infancy amid civil broil and bloodshed, soon imparted a barbarity unsurpassed in the annals of civil discord. The city of Edinburgh became filled with the loyalists: their leaders were Kirkaldy, Chatelherault, and Huntly; who, in addition to their vassals, retained in constant pay a hundred lances on horseback, and five hundred foot, commanded by Captains David Melville, Montgomery, Hamilton, Bruce, and Lauder, who was also sergeant-major of the city trained bands. These were brave but mercenary troops, and were independent of Kirkaldy’s soldiers, who amounted to rather more than half their number.

About the time that the Earl of Sussex, with an English army, carried fire and sword through all the fertile Merse and beautiful Teviotdale, giving fifty castles and three hundred villages to the flames, and Sir William Drury, with the old bands of Berwick, carried equal devastation through Clydesdale — both wanton inroads, which the convulsed state of the country prevented it from revenging—Morton advanced to Edinburgh with a considerable body of the crown vassals, for the purpose of driving out the queen’s faction. The English invasion had put Kirkaldy on the alert: confidently anticipating a siege, he had made additions to the strength of the castle, and obtained fresh supplies; but, on hearing of Morton’s march from the west, he resolved to commence hostilities without delay.

With two of his heaviest pieces of ordnance, and a hand of harqucbussiers, he marched from the castle, and placed them in ambush at a place overlooking the Glasgow road, by which he expected his enemy Morton to approach. The latter soon appeared riding at the head of his pikemen, when suddenly Kirkaldy gave the word, and the loaded and pointed culverins belched forth their contents from the foliage which concealed them. Struck hy a panic the king’s soldiers faced about and fled; and Morton “was so startled,” according to an old writer, that he did not molest Edinburgh for a considerable time afterwards. Meanwhile Sir William Drury, after committing frightful ravages on the lands of the queen’s adherents, had retired leisurely to Berwick without menacing the capital, as its martial provost had fully anticipated he would.

During an abstinence from hostilities which took place for two months, he was involved in several disagreeable broils with the irascible and turbulent burghers of Edinburgh, into which he was hurried by the military impetuosity of his temper, the dangerous and peculiar nature of his position, and, above all, by his zeal for the captive Mary. Among the citizens he carried matters with a very high hand; the disgusts increased between them, and the solemn Mutual Bond, signed in 1568, was now forgotten, or deemed a dead letter.

The expected succours from abroad dwindled down to six hundred helmets, as many harquebusses and pikes, seven pieces of cannon, and a sum of money which the Duke of Alva sent to Edinburgh, and for which Lord Seaton, and John Hamilton rector of Dunbar, were sent to Madrid to express the thanks of their party to the king of Spain.

Towards the end of the year 1570, Kirkaldy became involved in a quarrel with his old friend Knox, the Reformer, the circumstances of which were as follow:—

John Kirkaldy, son of Patrick, Sir William’s uncle, (the same young man in whose cause he fought with Ralph Evers,) had a brawl with a young cavalier named George Durie, son of Durie of that Ilk, commendator of Dunfermline. The immediate cause of the quarrel was in consequence of John Kirkaldy being summoned to compear in the justice court of Dunfermline, as member of an assize, when he was assailed in the hall by young Durie, Henry Seaton, and other gentlemen, sword in hand. He defended himself bravely, hut, had the provost not interfered, would inevitably have been slain, as he was without armour—a very unusual circumstance in those times. It is probable that the old gift of the Duries’ castle of Wester-Kinghom was the primary cause of this feud; but Sir William Kirkaldy, in his “ Complaint to the kirk-session of Edinburgh,” sets forth 11 that the house of Durie had done many injuries to him and his; that the chief of that name was author of the death of his goodsire the Laird of Raith, and of the ruin of his house; and that, since that time, they have continually troubled his posterity and friends in their rightful titles, native rowmes, and old possessions.”

He was highly exasperated at the attempt to slay his nephew; and, understanding that Henry Seaton was in the city on private business, he sent six soldiers or valets with orders to truncheon him, but gave them strict injunctions not to draw their swords. He did not anticipate what was to ensue. The chastisers traced Seaton to Leith, where he was about to embark for Fife, after having transacted his business in the city. As he threaded his way among the kail-yards, cottages, anchors, boats, &c. which then encumbered the banks of the river, instead of the well-bulwarked piers of the present day, a soldier approached, and presented or struck him with a baton.

Enraged by this act of hostility and insult, young Seaton drew his long rapier, and rushed upon him to revenge it. Kirkaldy’s valets drew in turn, and then ensued a sharp conflict, which ended by Seaton being repeatedly run through and slain, as he stumbled backward over a cable and anchor on the beach. This occurred ere any of the spectators could come to his rescue; he was left lying dead by the water side, while his slayers retreated with the utmost expedition. But news of the outrage reached the city before them. Headed by their bailies, a body of armed citizens attempted to intercept their retreat to the castle; five cut their way through and gained its gates in safety; but James Fleming was captured, and imprisoned in the Tolbooth.

Kirkaldy, whose garrison was probably recruited from his own vassalage, highly valued this man, and considered his seizure as an affront upon himself, which, as provost of the city, and governor of a castle whose guns could have ruined it in an hour, and from the revengeful spirit of the time, could not he overlooked. He determined to rescue him.

Therefore late in the night of the 21st December, when the citizens were all retired to their houses, he made due preparations, without and within the fortress, to save James Fleming. “Without, he had the deaconis of craftis, and all the rable of craftismen, readie for vproare and tumult;” within, he had his numerous cannon shotted, and his soldiers arrayed in their armour. With a chosen party, and a strong battering-ram to break down the doors of the prison, he marched into the city; to prevent the sudden alarm of which he had the precaution to send soldiers to seize the great bell of St Giles, which, by its iron notes, usually roused the whole citizens like a nest of armed hornets.

The wintry night was intensely dark. Lord Home, sheathed in armour, with a band of harquebussiers and pikemen, kept guard at the upper tron to prevent Kirkaldy’s retreat being cut off; while he, with the Laird of Dry law, assailed the picturesque Tolbooth, against the strong door of which the men-at-arms thundered with the battering-ram. The javelleur, or gudeman of the prison-house, resolutely refused them admission; but the ram soon did its work. The oaken barrier was dashed to fragments — the soldiers rushed in and bore off their comrade in triumph, together with another prisoner, a female, suspected of cognisance of the assassination of the Regent Murray. Kirkaldy ordered her to be conveyed to the castle, the heavy cannon of which Pitarrow, the constable, in a spirit of mischief, had repeatedly discharged to increase the uproar, "whereby the town was put in great fear; John Wallace’ hous was schot through, and a harne beaten down in the Cannogait,” as Banna-tyne records—a fact which shows the limited extent of the Scottish capital, when bam-yards were within range of a cannon from its castle.

When his friend Cecil, then created Lord Burghley, heard of these passages, he remonstrated with Kirkaldy in severe terms, expressive of the surprise they occasioned him.

“How you will allow my plainness,” he continues, in a letter addressed to him, “I know not; but I should think myself guilty of blood if I should not thoroughly dislike you; and to this I must add that I hear—but yet am loth to believe it—that your soldiers that broke the prison have not only taken out the murderer, your man, hut a woman that was detained as guilty of the lamentable death of the last good regent. Alas! my lord, may this he true? And, with your help, may it be conceived in thought that you—you, I mean, that was so dear to the regent—should favour his murderers in this sort?”

But neither the eloquence of the English minister, nor the virulence of Knox, softened Kirkaldy in the least, or prevailed upon him to acknowledge himself in error. As civil and military governor of Edinburgh, he considered himself superior to its magistrates, and entitled to keep any prisoner in his own possession. Three days after Fleming’s rescue, Knox preached in the church of St Giles, and failed not to reprove “sic disorder;” affirming that he had never, (during all the troubles he had witnessed,) "seen so sclanderous, so malapert, so fearful, and so tyrannous a fact!” and, fearless of Kirkaldy’s pride and indignation, the stern Reformer, warming with his discourse, continued to condemn, in strong language, the riot of the night and violation of the house of justice. Had it been done by a bloodthirsty man, who was without the fear of God, he would not, (he said,) have been so much moved at it; but he was affected to think that Sir William Kirkaldy of the Grange,—one of whom all good men had formed such great expectations, should have fallen so far as to act a part so vile,—he who, when a captive in the castle of Mont Saint Michel, had refused to purchase even his liberty at the price of human blood!

An erroneous and exaggerated account of this sermon being conveyed to Kirkaldy, he was highly incensed at the preacher’s daring and presumption; and assuming the pen, which he wielded as well as the sword, sent the following letter forthwith to Knox’s colleague, Master John Craig:—

“This day John Knox, in his sermon, openly called me a 'murderer and a throat-cutter,’ wherein he has spoken further than he is able to justify; for I take God to be my witness, if it was my mind (intention) that man’s blood should have been shed of whom he has called me murderer: and the same God I desire, from the bottom of my heart, to pour out his sudden vengeance upon him or me, whether of us twa have been most desirous of innocent blood. This I desire you, in God's name, declare openly to the people!

“At the castle of Edinburgh, 24th December 1570.”

This forcible epistle was delivered by a soldier to Master Craig in the pulpit of St Giles’s church; but he, having the inflexible Reformer to dread on one hand, and the haughty governor on the other, prudently declined to read the letter without the consent of the kirk; upon which the Knight of Grange took the very peaceable mode of obtaining redress by applying to the kirk-session, requiring that his honour should be vindicated as publicly as it had been traduced. Knox, on learning that his words had been misrepresented, and that Kirkaldy continually affirmed his innocence of any intent to slay Henry Seaton, embraced the first opportunity to explain his true meaning from the pulpit. The explanation was not satisfactory; the old friendship between them was never renewed, and Kirkaldy, on a subsequent Sunday, made a display which was deemed decidedly hostile to Knox. After having been absent from church nearly a whole year, (which alone was a nameless atrocity in the eyes of the Reformed clergy,) he suddenly marched into St Giles’s, with a train composed of the same soldiers who had been engaged in Seaton’s death and Fleming’s rescue. Though he came to church thus attended, merely out of compliment to Margaret countess-dowager of Murray, who was that day to hear Knox preach, the stern minister regarded his presence and retinue as an attempt to set him at defiance, or overawe his discourses, which were generally levelled against Mary and her adherents. In no way daunted by the clanking weapons and shining armour of the soldiers, in his sermon he dwelt particularly "on the sinfulness of forgetting benefits received from God;” and, turning his discourse to bear on late events, warned his hearers against confiding in the mercy of Heaven while infringing its commandments, “and proudly defending such transgression.”

Enraged at the admonitions which, like Knox’s glances, he knew were levelled at himself, Kirkaldy started up, regardless of the place, the countess, and congregation, and so far forgot his usual dignity as to make use of very threatening language against the aged preacher. A report soon spread that he had become his enemy, and would slay him as he had done Seaton; but though nothing could be farther from the mind of so gallant a knight, it gained ground so far that the noblesse of Kyle and Cunninghame sent him a formal letter, in which, after reminding him of his former adherence to the cause of the Reformation, they mentioned the late rumours that had reached them, and solemnly warned him of any attempts to injure Knox, “that man whom God had made the first planter and waterer of his church among them.” It was sent from Ayr, and bore the signatures of Knox’s father-in-law, Lord Ochiltree, the Earl of Glencaim, and eleven lesser barons.

But Kirkaldy had more important duties to attend to than prosecuting a quarrel with a preacher. Unintimidated by the fulminations of kirk and state, he continued his warlike preparations with the utmost deliberation and success. He hoisted cannon to the summit of St Giles’s lofty spire, which rises in the middle of the central hill on which the city stands, and commands a view of it in every direction. He placed the artillery on the stone bartizan beneath the flying arches of the imperial crown that surmounts the tower, and thus turned the cathedral into a garrison, to the great annoyance of Knox and the citizens. The latter were also compelled, at their own expense, to maintain the hundred harquebussiers of Captain Melville, who were billeted in the Castlehill Street, for the queen’s service; and thus, amid preparations for war, closed the year 1570.