On August 25th Protestantism was proclaimed and Catholicism suppressed in Scotland by a convention of states assembled without the assent of the absent Queen. On December 5th Francis II died; in August, 1561, his widow left France for Scotland, having been refused a safe-conduct by Elizabeth on the ground of her own previous refusal to ratify the treaty made with England by her commissioners in the same month of the preceding year. She arrived nevertheless in safety at Leith, escorted by three of her uncles of the house of Lorraine, and bringing in her train her future biographer, Brantome, and Chastelard, the first of all her voluntary victims. On August 21st she first met the only man able to withstand her; and their first passage of arms left, as he has recorded, upon the mind of John Knox, an ineffaceable impression of her "proud mind, crafty wit, and indurate heart against God and his truth."

And yet her acts of concession and conciliation were such as no fanatic on the opposite side could have approved. She assented, not only to the undisturbed maintenance of the new creed, but even to a scheme for the endowment of the Protestant ministry out of the confiscated lands of the Church. Her half-brother, Lord James Stuart, shared the duties of her chief counsellor with William Maitland of Lethington, the keenest and most liberal thinker in the country. By the influence of Lord James, in spite of the earnest opposition of Knox, permission was obtained for her to hear mass celebrated in her private chapel—a license to which, said the reformer, he would have preferred the invasion of ten thousand Frenchmen.

Through all the first troubles of her reign the young Queen steered her skilful and dauntless way with the tact of a woman and the courage of a man. An insurrection in the North, headed by the Earl of Huntly under pretext of rescuing from justice the life which his son had forfeited by his share in a homicidal brawl, was crushed at a blow by the lord James against whose life, as well as against his sister's liberty, the conspiracy of the Gordons had been aimed, and on whom, after the father had fallen in fight and the son had expiated his double offence on the scaffold, the leading rebel's earldom of Murray was conferred by the gratitude of the Queen. Exactly four months after the battle of Corrichie, and the subsequent execution of a criminal whom she is said to have "loved entirely," had put an end to the first insurrection raised against her, Pierre de Boscosel de Chastelard, who had returned to France with the other companions of her arrival, and in November, 1562, had revisited Scotland, expiated with his head the offence of the misfortune of a second detection at night in her bedchamber.

In the same month, twenty-five years afterward, the execution of his mistress, according to the verdict of her contemporaries in France, avenged the blood of a lover who had died without uttering a word to realize the apprehension which, according to Knox, had before his trial impelled her to desire her brother "that, as he loved her, he would slay Chastelard, and let him never speak word." And in the same month, two years from the date of Chastelard's execution, her first step was unconsciously taken on the road to Fotheringay, when she gave her heart at first sight to her kinsman Henry, Lord Darnley, son of Matthew Stuart, Earl of Lennox, who had suffered an exile of twenty years in expiation of his intrigues with England, and had married the niece of King Henry VIII, daughter of his sister Margaret, the widow of James IV, by her second husband, the Earl of Angus. Queen Elizabeth, with the almost incredible want of tact or instinctive delicacy which distinguished and disfigured her vigorous intelligence, had recently proposed as a suitor to the Queen of Scots her own low-born favorite, Lord Robert Dudley, the widower if not murderer of Amy Robsart; and she now protested against the project of marriage between Mary and Darnley.

Mary, who had already married her kinsman in secret at Stirling castle with Catholic rites celebrated in the apartment of David Rizzio, her secretary for correspondence with France, assured the English ambassador, in reply to the protest of his mistress, that the marriage would not take place for three months, when a dispensation from the Pope would allow the cousins to be publicly united without offence to the Church. On July 29, 1565, they were accordingly remarried at Holyrood. The hapless and worthless bridegroom had already incurred the hatred of two powerful enemies, the Earls of Morton and Glencairn; but the former of these took part with the Queen against the forces raised by Murray, Glencairn, and others, under the nominal leadership of Hamilton, Duke of Châtelherault, on the double plea of danger to the new religion of the country, and of the illegal proceeding by which Darnley had been proclaimed king of Scots without the needful constitutional assent of the estates of the realm.

Murray was cited to attend to the "raid" or array levied by the King and Queen, and was duly denounced by public blast of trumpet for his non-appearance. He entered Edinburgh with his forces, but failed to hold the town against the guns of the castle, and fell back upon Dumfries before the advance of the royal army, which was now joined by James Hepburn, Earl of Bothwell, on his return from a three years' outlawed exile in France. He had been accused in 1562 of a plot to seize the Queen and put her into the keeping of Earl of Arran, whose pretensions to her hand ended only when his insanity could no longer be concealed. Another new adherent was the son of the late Earl of Huntly, to whom the forfeited honors of his house were restored a few months before the marriage of his sister to Bothwell. The Queen now appealed to France for aid; but Castelnau, the French ambassador, replied to her passionate pleading by sober and earnest advice to make peace with the malcontents. This counsel was rejected, and in October, 1565, the Queen marched an army of eighteen thousand men against them from Edinburgh; their forces dispersed in face of superior numbers, and Murray, on seeking shelter in England, was received with contumely by Elizabeth, whose half-hearted help had failed to support his enterprise, and whose intercession for his return found at first no favor with the Queen of Scots.

But the conduct of the besotted boy, on whom at their marriage she had bestowed the title of king, began at once to justify the enterprise and to play into the hands of all his enemies alike. His father set him on to demand the crown matrimonial, which would at least have assured him the rank and station of independent royalty for life. Rizzio, hitherto his friend and advocate, induced the Queen to reply by a reasonable refusal to this hazardous and audacious request. Darnley at once threw himself into the arms of the party opposed to the policy of the Queen and her secretary—a policy which at that moment was doubly and trebly calculated to exasperate the fears of the religious and the pride of the patriotic. Mary was invited if not induced by the King of Spain to join his league for the suppression of Protestantism; while the actual or prospective endowment of Rizzio with Morton's office of chancellor, and the projected attainder of Murray and his allies, combined to inflame at once the anger and the apprehension of the Protestant nobles.

According to one account, Darnley privately assured his uncle George Douglas of his wife's infidelity; he had himself, if he might be believed, discovered the secretary in the Queen's apartment at midnight, under circumstances yet more unequivocally compromising than those which had brought Chastelard to the scaffold. Another version of the pitiful history represents Douglas as infusing suspicion of Rizzio into the empty mind of his nephew, and thus winning his consent to a deed already designed by others.

A bond was drawn in which Darnley pledged himself to support the confederates who undertook to punish "certain privy persons" offensive to the state, "especially a stranger Italian called Davie"; another was subscribed by Darnley and the banished lords, then biding their time in Newcastle, which engaged him to procure their pardon and restoration, while pledging them to insure to him the enjoyment of the title he coveted, with the consequent security of an undisputed succession to the crown, despite the counter-claims of the house of Hamilton, in case his wife should die without issue—a result which, intentionally or not, he and his fellow-conspirators did all that brutality could have suggested to accelerate and secure.

On March 9th the palace of Holyrood was invested by a troop under the command of Morton, while Rizzio was dragged by force out of the Queen's presence and slain without trial in the heat of the moment. The parliament was discharged by proclamation issued in the name of Darnley as king; and in the evening of the next day the banished lords, whom it was to have condemned to outlawry, returned to Edinburgh. On the following day they were graciously received by the Queen, who undertook to sign a bond for their security, but delayed the subscription until the next morning under plea of sickness. During the night she escaped with Darnley, whom she had already seduced from the party of his accomplices, and arrived at Dunbar on the third morning after the slaughter of her favorite. From thence they returned to Edinburgh on March 28th, guarded by two thousand horsemen under the command of Bothwell, who had escaped from Holyrood on the night of the murder, to raise a force on the Queen's behalf with his usual soldierly promptitude.