Cecil had personal reasons for watching the intrigue for the marriage of Mary with the Duke of Norfolk. The Earl of Leicester, always jealous of the influence of the great Minister with his mistress, endeavoured secretly to undermine a power which he dared not attack face to face, and he exerted himself to attach the powerful Norfolk by urging him on in his perilous undertaking. The duke hesitated, but the Earl of Arundel and the Earl of Pembroke united themselves with Leicester. They despatched to Queen Mary articles of marriage, intended to insure the security of Elizabeth, by the total renunciation by Mary of her pretensions to the crown of England, and by an alliance, offensive and defensive, with the queen, her good sister. Mary Stuart was to allow the reformed religion to be established in Scotland, and to give her hand to the Duke of Norfolk.

People who are anxious to get out of prison are ready to accept harsh conditions, especially when they are not firmly resolved to observe them. Mary promised all that was desired with the sole reservation that the consent of Elizabeth should be obtained to the marriage. "All my misfortunes," she said, "have arisen from the anger of my sister, when I married Darnley." Leicester was counted upon to obtain this favour, and the duke wrote the most passionate letters to Mary, through the agency of the Bishop of Ross, who was still faithful to his mistress. The consent of the Kings of Spain and France had been asked for, and Murray was to propose to the Parliament of Scotland the liberation of the Queen.

He proposed it, in effect, though probably without any great sincerity. Mary had brought many misfortunes and few benefits to Scotland, and her brother had not that attachment for her which causes all other considerations to be forgotten. The articles coming from England were rejected; the question of the divorce which Bothwell had caused to be declared in Denmark was not even examined, and Queen Elizabeth was warned of what was preparing in the dark. She was at Farnham; the rumour of the marriage circulated at the court. Leicester had taken no step with regard to it as yet. Norfolk was there, not daring to go away; he dined at the table of the queen, who one day said to him, with a significant look, which reminded him of his own words, "Good evening, my lord duke; be careful upon what pillow you rest your head." Norfolk took alarm. A few days afterwards, the court was at Titchfield. Leicester fell ill; the queen hastened to his bedside, and there impelled by remorse and keeping up the farce of passion, Leicester avowed to her with tears that he had acted disloyally towards her, by endeavouring, unknown to her, to marry her rival to the Duke of Norfolk. Leicester obtained his pardon, but the royal displeasure rested upon the Duke of Norfolk. The disfavour of Elizabeth was dangerous; the Duke retired to Kenninghall, whence he was soon recalled. A French servant of Mary Stuart, arrested in Scotland, had, it is said, made fresh revelations upon the complicity of his mistress in the murder of Darnley; the servant was executed, but the imprisoned queen remained exposed to the anger and indignation of Elizabeth. An insurrection in the North was feared, for the Earls of Arundel and Pembroke had both quitted the court. Norfolk was conducted to the Tower; the Bishop of Ross was arrested, although he pleaded the privilege of an ambassador, and all the noblemen compromised in the intrigue received an order to retire to their homes. The anxieties of Elizabeth, real or feigned, were not without some foundation. The Catholics of her kingdom, groaning under a secret but cruel oppression, naturally turned towards the Queen of Scotland, in their eyes the legitimate heiress to the throne, sanctified by her misfortunes, surrounded by the double fascination of her charms and of that faith towards which she had always manifested the most sincere attachment. The Huguenots had recently suffered great disasters at the battle of Jarnac, where the Prince of Condé had been killed, and also at the battle of Moncontour. The English noblemen whom the queen had gradually allowed to pass into the service of the French Protestants were compelled to return to England, whither they brought gloomy tales of the cruelty of the victorious Catholics, and of their resolve to cause Catholicism to triumph everywhere, no matter by what means. To complete the hostility of the Continent, Queen Elizabeth, always greedy for money, had taken possession in time of peace of a fleet of Spanish galleons, bearing to the Duke of Alba the sums sent him by the King of Spain, which fleet had taken refuge upon the coast in order to escape the Huguenot vessels. It was pretended, at the court of England, that the money did not belong to Philip II., but to some Genoese and Lombard bankers, who could have no objection to lend it to Queen Elizabeth. The vessels of the English merchant navy had all become pirates, stopping and pillaging Spanish and French ships, seconding the attempts and projects of the Huguenots upon all coasts, and bringing arms and supplies to them. Some convoys setting out for La Rochelle were even accompanied by royal vessels, and the queen secretly authorized a great number of noblemen to take service in the army of the Huguenots, or in that of the Prince of Orange, while she replied to the complaints of the Spanish and French ambassadors by the assurance of her friendship for their sovereigns and of her wish to preserve the peace. Treachery was met by treachery. A conspiracy, half Spanish, half French, was preparing upon the Continent, to encourage the insurrection of the Catholics. Ridolfi, an agent sent from Italy, had communication with the Duke of Alba on passing through the Low Countries. Evil designs were secretly meditated against the life of Elizabeth, and the representations of the governor-general, who did not believe in the possibility of success, having had no effect upon his master, the intrigue was developed in the north of England; the tyranny of Elizabeth had itself paved the way for it.

Captive princes always find means of communicating with their partisans, however close may be their prison, and however strict the supervision may appear. Mary Stuart had entered into relations with all the great Catholic noblemen of Yorkshire, Durham and Northumberland. An attempt at escape had even been organized, which was to place her at the head of her little army, but the project collapsed, and, on the 16th of November, 1569, the Earls of Northumberland and Westmoreland, with a great number of noblemen and retainers, raised the standard of revolt, with the intention of marching upon Tutbury, to deliver and proclaim the captive queen. Upon the way the insurgents burnt in the churches the prayer books, while announcing everywhere that the Catholic religion was re-established, and summoning all good Catholics to join them. But Mary had already been transferred from Tutbury to Coventry. The populations did not respond to the appeal of the rebels; the southern counties took up arms against them. A goodly number of Catholics joined the royal army, assembled at York. Uneasy and irresolute, the two earls fell back upon Praby Castle. They besieged Sir George Bowes, in Barnard Castle, compelled him to capitulate, and planted themselves in the little port of Hartlepool, hoping to receive Spanish assistance through the Low Countries.

Meanwhile the Earl of Sussex, who had delayed so long at York that suspicions had been aroused as to his loyalty, was at length advancing against the rebels with the reinforcements which the Earl of Warwick had brought him. The insurgents fell back slowly towards the frontier of Scotland, and soon took refuge, without fighting, in that kingdom, the support of which they had hoped for. Elizabeth at once demanded the surrender of all the chiefs. Murray could not or would not satisfy this requirement. The Earl of Northumberland alone was in his hands. The Earl of Westmoreland, Egremont, Ratcliff, and the other great noblemen were in safety at the residences of their Scottish friends, who furnished them with means to reach the Low Countries. The regent sent his prisoner to Lochleven, saying that he would exchange him for Queen Mary; but before the negotiation had begun, even before Lord Leonard Dacre, the last of the insurgents who still held out in England, had been in his turn obliged to take refuge in Scotland, Murray was assassinated on the 22nd of January, 1570, in the streets of Linlithgow, and Queen Elizabeth wreaked her vengeance upon the counties which had taken part in the insurrection. "There are so many guilty persons to condemn," wrote the Bishop of Durham to Cecil, "that difficulty is experienced in finding enough men innocent of all rebellion, to make juries of them." A royal declaration was read in all the churches in the peaceful districts, as well as in the regions bristling with gibbets, reminding the people of the peaceful years which England had enjoyed under the reign of Elizabeth, and affirming that she claimed, as chief of the Church, no other authority than that which her predecessors had exerted, her noble father, King Henry VIII., and her dear brother, King Edward VI. She did not intend to put a constraint upon the conscience of her subjects, provided the Christian religion, as it was established in the acts of faith, should in nowise be molested, and that people should conform themselves to the laws of the kingdom, for the practice of public worship. Liberty, as understood by Queen Elizabeth, consisted in doing exactly as she commanded.

The death of Murray, the only man sufficiently skilful and influential to maintain a little order in unhappy Scotland, had again delivered up that kingdom to the dissensions of parties. The Duke of Chatellerault and the Earl of Argyle immediately took possession of the government in the name of Queen Mary; but Morton, at the head of the king's men, as the partisans of James VI. were called, had taken up arms, summoning England to his aid. Elizabeth sent him an army and a regent. She had taken back into favour the Earl of Lennox, father of Darnley, and grandfather of the little king, and despatched him to Scotland, to govern in the name of his grandson, while the English troops entered several times into Scotland, devastating all the southern counties, burning down the towns and villages, and supporting the efforts of the new regent, who was implacable in ravaging the domains of the Duke of Chatellerault and of all the family of the Hamiltons. When Sir William Drury returned to Berwick, on the 3rd of June, after the recent campaign, the ravages had been so great, that the authority of Lennox appeared to be established upon the ruin of all his adversaries.

The Catholic arms had failed as well as the Catholic conspiracies. Pope Pius V. was anxious to try the spiritual thunders of the Vatican. A bull declaring the excommunication of Elizabeth, depriving her of her pretended rights to the crown of England, and absolving her subjects from their allegiance, had been prepared for some time; it was signed after the insurrection had failed, and several copies of it were sent to the Duke of Alba; but Philip II. prohibited the publication of them in the Low Countries. On the 13th of May, 1570, however, the bull was posted upon the door of the palace of the Bishop of London. During the investigations which were immediately made in courts of law, of evil notoriety both in political and religious affairs, it was ascertained from a student under torture, that he had received a copy of the bull from a rich Catholic gentleman named Felton. The latter was arrested, and he avowed without hesitation that he had posted up the bull, but no punishment could make him reveal the names of his accomplices. Being condemned to a traitor's death, he walked to the place of execution as to a martyrdom, designating the queen by the name of "Pretender," and remaining firm in his enthusiasm until the last moment. Before his death, and while upon the scaffold, however, he asked that the pardon of Elizabeth might be solicited for aught in which he might have offended her, and sent her, as a token a magnificent ring of great value, which he took from his finger. Even among those who contended against her with the greatest tenacity, Elizabeth contrived to win from her people so sincere and loyal an affection, that condemned persons sent presents to her, and criminals whom she had caused to have a hand cut off for having written against her, seized their hats with their left hands and waved them above their heads, exclaiming, "God bless Queen Elizabeth!"