In reply to this appeal, which it was difficult to reject with common justice, Mary was transferred from Carlisle to Bolton Castle. The agents of Elizabeth, in all the courts of Europe, appeared to have given the signal to each other to alarm her concerning the consequences of the liberation of the Queen of Scotland. "Her Grace now holds the wolf who wished to devour her," wrote, from Paris, Sir Henry Norris; "it is said that there is a conspiracy between the King of France, the King of Spain, and the Pope, to ruin her Majesty, and to put the Queen of Scotland in her place."

Elizabeth sent a messenger to Scotland, to call upon the regent and the confederate lords to cease hostilities; but her representations had little effect, while the manœuvres of the Scottish insurgents powerfully impressed her. She began to believe in the crime of which Mary so vigorously protested her innocence, and she demanded that the Queen of Scotland should exculpate herself in her eyes, promising to place her again upon the throne if her innocence should be proved; for, at the bottom of her heart, and in her royal sympathy for sovereigns, she had been and remained shocked at the audacity of the Scots, who had dared to dethrone their queen, whatever might have been her faults. The regent had replied to the reproaches and threats of the Queen of England, that "if Elizabeth wished to wage war against them, they would not sacrifice their lives, and would not risk their possessions, by passing as rebels in the world, when they had in their hands the means of justifying themselves, whatever regret that might occasion them."

The die was cast; the accusers of Queen Mary, her brother, Lord Murray, and his constant enemy, Lord Morton, were to come from Scotland, to be confronted with her before the commission of English judges. All parties were equally uncertain, respecting the result of the conference, for all distrusted Queen Elizabeth, who had lavished upon both sides the most contradictory promises. Mary counted upon her to replace her again upon her throne. "I have abandoned despatching my letters to the courts of France and Spain, relying upon the promises of your Grace, and wishing, if I am to be restored to the throne, that it may be solely by the means of the court of England." However, Cecil had assured Murray "that it was not intended to re-establish the Queen of Scotland, if her crime is proved, whatever her friends may say."

The conferences opened at York, upon the 4th of October. There were repeated all the arguments, there were enumerated all the facts well known in history. Mary threw the guilt of the crime not only upon Bothwell, but upon his accomplices, causing it to be clearly understood that her accusers had good reasons for making the whole weight of it fall upon her. She resolutely denied the genuineness of the letters found in her casket, of which copies only had been produced at first, and she demanded to be admitted to the queen, to defend herself in her presence. The conferences were transferred from York to Westminster. The Queen of England and her ministers felt the necessity for following more closely the dark intrigues which intersected each other in all directions around the captive queen. The secretary Maitland had opened negotiations for the marriage of the Queen of Scotland with the Duke of Norfolk, affirming that the Protestantism of the great English nobleman would reassure the reforming party in Scotland, and would definitively re-establish the throne of the Queen. It is probable that the designs of the skilful intriguer went further. He was aware of the secret discontent of the English Catholics, of the powerful friends whom Norfolk could rally around him, and he hoped no doubt to raise a revolt in England. The wisdom of Cecil saw through the manœuvre. The liberty of Mary was for ever lost, even could her innocence have been proven, which it assuredly was not. Mary in Scotland constantly threatened the throne of Elizabeth. The servants of the Queen of England were even alarmed for her life. Mary in prison was dangerous, no doubt, but the peril was less and the question of the justice of the detention of a sovereign who had voluntarily come to place herself under the protection of her relative, did not enter into the matter. On the 11th of January, 1569, after three months of conferences and intrigues, Elizabeth publicly declared to the Regent Murray that nothing had been proved against his honour or that of his partisans, but that the crimes imputed to Queen Mary had not been demonstrated with sufficient clearness to inspire her with a bad opinion of her good sister. Nevertheless, Murray returned freely to Scotland, supplied with the money which was necessary for the support of his government, and Mary remained in prison, in spite of her protestations and anger. Elizabeth several times found means of counselling her to abandon the crown and to lead a peaceful life in England, but Mary firmly replied that she was determined to die rather than to comply with such suggestions; that justice required that she should be reestablished upon her throne, after which "she would show as much clemency to the authors of her troubles, as should appear to her compatible with her honour and the good of her kingdom." The captive also protested that she would not consent to proceed further away from the frontier; but, on the 26th of January, in cold and gloomy weather, the beautiful queen was compelled to mount a wretched horse, and accompanied by a few ladies, and a small number of servants, to ride as far as Tutbury Castle in Staffordshire, a fortress belonging to the Earl of Shrewsbury. This nobleman was henceforth entrusted with her custody, a constant anxiety to the sovereign who under the influence of female jealousy had belied the nobler side of her character, and who now could find no place sufficiently strong, no jailor sufficiently vigilant to keep the prisoner whom she was unjustly detaining.

The affairs of Queen Elizabeth were as much complicated abroad as at home, and her external policy was neither frank nor sincere. The oppression of the United Provinces by the King of Spain had aroused a general discontent which brought about insurrections in the towns, and the beginning of that indomitable rebellion which was to end in the dismemberment of the Low Countries. The Prince of Orange had placed himself at the head of the oppressed people, protecting the religious and political liberties of his country, and his great struggle with the terrible Duke of Alba had begun. Everywhere the Protestants felt themselves threatened, and conspiracies recommenced in France. The Prince of Orange and the Prince of Condé both applied to Queen Elizabeth for assistance and money. The queen secretly supported them in a niggardly and unwilling fashion, though urged by Cecil, whose policy was more firm, whose intelligence was more clear-sighted, and whose views were broader than those of his mistress; but she took care loudly to protest her friendship for the King of Spain and Charles IX., while encouraging the open or secret enemies who were struggling against their power. Upon all stages and in all countries of Europe the policy of the sixteenth century continually presents that character of duplicity and falsehood which necessarily results from the absence of publicity and control, but which renders history difficult to understand, and more difficult to relate.

Amidst the embarrassments which the claimants of the succession to the crown of England caused her, Elizabeth had resumed, it, indeed, she had ever abandoned her matrimonial negotiations. The Archduke Charles was yet unmarried, and, in 1567, the queen solemnly sent the Earl of Sussex, as ambassador, to Vienna, to deal with the great question of religion. The archduke had never come to England, although he had several times been invited, and the queen declared that she would never marry a man without having seen him. Sussex lavished upon her descriptions of the person of the Archduke, not without adding to them the attraction of his domains, and of the great position which he occupied at the court of the Emperor. He assured the prince that this time the queen wished to proceed seriously in the matter, since she was free to marry whomsoever she should think fit, and she had never inclined towards any other union. The archduke felt much honoured, but when the question of religion was opened, he frankly declared that his ancestors had always professed the same religion as himself, that he knew no other, and would never change it. Elizabeth then urged the Protestant feeling of her subjects, without, however, breaking off the negotiations, which only ended on the day when the archduke married the daughter of the Duke of Bavaria.

The embarrassments of Elizabeth in England were complicated through the progress of the intrigue having for its object the marriage of Mary with the Duke of Norfolk. Elizabeth had openly spoken of it to the Duke, who had excused himself, affirming that he could never think of uniting himself to a princess who had raised claims to the throne of England, nor to a woman whose husband could not sleep peacefully upon his pillow. This allusion to the fate of Darnley had for a moment lulled the distrust of the Queen of England, but Cecil was alive to all the dangers which threatened his mistress. He had a short time before discovered the marriage of Lady Mary Grey, sister of Lady Jane and Lady Catherine. "What a mischance!" he wrote; "Sergeant Portier, the tallest and fattest of the gentlemen of the court, has conceived the idea of secretly marrying Lady Mary Grey, the shortest of all the ladies. They have been placed in separate prisons, the crime being very great." And the jealousy of Elizabeth towards any who approached the throne closely, or at a distance, was so excessive, that the unhappy Mary remained in prison until her death, without ever seeing her husband again. Deplorable end of a family doomed to the most tragic reverses!