Mary could not possibly be happy in such circumstances. Whatever might be the state of her conscience, her character was fearfully implicated, and on all sides came calls for inquiry, which she did not seem to have the power or the will to make. The climax to her trouble was put by the queen-mother of France and her uncle, the cardinal, sending her the most cutting message of reproach; calling on her without delay to avenge the death of the king, and to clear her own reputation, or regard them as no longer her friends, but the proclaimers of her utter disgrace. There was no possibility of delaying inquiry any longer, but every means was adopted to make it a mockery. Lennox was forbidden to appear with more than six followers, and his efforts to obtain a postponement were fruitless. In his absence Bothwell was unanimously acquitted.

Rumours now arose that Bothwell was about to divorce his wife, the sister of Huntly—to whom he had been married only six months—and to marry the queen; and in the face of these reports Mary conferred on him the castle and lordship of Dunbar, with extension of his powers as Lord High Admiral. As tidings of the queen's intended marriage grew, Murray, her brother, stole away out of contact with danger or responsibility and retired to France. But, nevertheless, she did not lack warning. Her ambassador at the French Court entreated her, in the most serious manner, to punish her husband's murderers, and not allow the world to use such freedom with her character as it did. She had equally strong letters from her friends in England, which Melville showed to her, and was advised by Maitland of Lethington to get away from Court for fear of Bothwell. Bothwell, however, soon put the matter beyond doubt. He invited the principal nobility to a tavern, kept by one Ainslie, and there he drew out of his pocket a bond expressing his innocence of the murder of Darnley, as established by the bench and the legislature, and his intention to marry the queen, and containing, it is said, her written warrant empowering him to propose the matter to the nobility. The company was composed partly of his friends and accomplices. The rest were taken with confusion, but they had all been deeply drinking, and they found the house surrounded by 200 of Bothwell's hackbutters. Under constraint, eight bishops, nine earls, and seven lords, subscribed the paper.

But the daring ambition of the man now roused even his old accomplices to conspire against him, for the safety of the young prince and Government. Morton, Argyll, Athole, and Kirkaldy of Grange, were at the head of this plot; and they wrote to Bedford the day after the supper at Ainslie's, saying it was high time that his dangerous career was checked, and engaging by Elizabeth's aid to avenge the murder of the king. Kirkaldy, who was the scribe, added that the queen had been heard to say that "she cared not to lose France, England, and her own country for him, and would go with him to the world's end in a white petticoat, before she would leave him."

An anonymous letter, but undoubtedly from some of this party, soon followed, declaring that the queen had concerted with Bothwell the seizure of her person. The correctness of this information was immediately proved. On Monday, the 21st of April, the very day foretold, Mary rode to Stirling to visit her son, where the Earl of Mar, entertaining strong suspicions of her intentions, refused to allow her access to him with more than two attendants, to her great indignation. On her return, as had been foreseen in the letter quoted, Bothwell met her at the head of 1,000 horse, at Almond Bridge, six miles from Edinburgh; and, according to Melville, who was in the queen's train, taking the queen's bridle, he boasted that "he would marry the queen, who could or who would not; yea, whether she would herself or not." He says that Captain Blackadder, one of Bothwell's men, told him that it was with the queen's own consent. Whether this were so or not, has been argued eagerly on both sides, but it is probable from what we have seen, that Mary really was a consenting party. The royal retinue was suffered to continue its journey, with the exception of Melville, Maitland, and Huntly, who were conducted along with the queen to the castle of Dunbar, the recent gift of Mary to Bothwell. The queen seems to have made no loud outcries against her apparently forcible abduction, and the country was so convinced of the sham nature of the affair, that there was no attempt to rescue her.

The divorce of Bothwell from his wife was now hastened, and after detaining the queen five days at the castle of Dunbar, he conducted her to Edinburgh, and led her to the castle, where she was received with a salute of artillery, Bothwell holding her train as she dismounted. The ministers of the Church were ordered to proclaim the banns of marriage between the queen and Bothwell, but they declined; and Craig, the colleague of Knox, who was absent, declared that he had no command from her Majesty, who was held in disgraceful constraint by Bothwell. This brought to him the Justice Clerk with a letter under the queen's own hand, stating that the assertions he had made were false and commanding him to obey. Craig still refused till he had seen the queen herself; and, before the Privy Council, charged Bothwell with murder, rape, and adultery. No punishment followed so daring a charge, and the preacher having done his duty, obeyed the Royal mandate and published the banns, at the same time exclaiming, "I take heaven and earth to witness that I abhor and detest this marriage, as odious and slanderous to the world; and I would exhort the faithful to pray earnestly that a union against all reason and good conscience may yet be overruled by God to the conform of this unhappy realm."

Nothing moved by these public expressions of censure and disgust, the queen appeared, on the 12th of May, at the high court of Edinburgh, and informed the Chancellor, the judges, and the nobility that, though she was at first incensed against the Earl of Bothwell for the forcible detention of her person, she had now quite forgiven him for his subsequent good conduct. That day she created Bothwell Duke of Orkney and Shetland, and with her own hand placed the coronet on his head. On the 15th they were married, at four o'clock in the morning, in the Presence Chamber of Holyrood. The ceremony was performed by the Bishop of Orkney, according to the Protestant form, Craig being present; and afterwards privately, according to the Romish rite.

Very soon circumstances hastened the inevitable insurrection in Scotland. Mary had summoned her nobles to accompany her on an expedition to Liddesdale, but many disobeyed the order. Murray had now arrived in England, and was using all his influence with Elizabeth to make a movement for the expulsion of Bothwell from his usurpation; and even Maitland, who to the last had remained at Court, wearing the air of a staunch supporter of the queen, slipped away and joined the opposition. These were ominous circumstances, and suddenly, while the queen and Bothwell were at Borthwick Castle, about ten miles from Edinburgh, the conspirators made a rapid night march, and morning saw the castle surrounded by nearly 1,000 Borderers, under the command of Hume and other Border chiefs, with whom were Morton, Mar, Lindsay, Kirkaldy, and others of the nobles.

The confederates deemed the queen and Bothwell now safe in their hands, but they were deceived. Bothwell escaped through a postern to Haddington, whence he reached Dunbar; and the queen also eluding them disguised as a man, rode booted and spurred after him. The confederates, disappointed of their grand prize, marched on the capital, forced the gates, and entered, proclaiming that they came to revenge the death of the king, and to rescue the queen from the murderer. There the Earl of Athole and Maitland joined them, and a banner was displayed on which was painted the body of the murdered king lying under a tree, and the young prince kneeling beside it, exclaiming, "Judge and avenge my cause, O Lord!" The people flocked to this exciting standard, and the leaders speedily commanded a strong force.

Mary and Bothwell, meanwhile, summoned the nobles and people around Dunbar, and the Lords Seton, Yester, and Borthwick, appeared in arms, with a body of 2,000 men. Impatient to quell the confederates at once, they marched to Seton, where Mary issued a proclamation, declaring that all the pretences of the confederates were false; that her husband, the duke, was no murderer but had, as they knew, been fully acquitted; she was under no restraint but freely married to Bothwell, by consent and approbation of these very nobles; nor was her son in any danger, unless it were from them, for he was in their hands. Mary advanced and entrenched herself on Carberry Hill, in the old works which the English had thrown up before the battle of Pinkie.

The confederates marched out of Edinburgh and confronted the Royal army, eager for the battle. De Croc, the French ambassador, now attempted to mediate between the two parties, and carried a message to Morton and Glencairn, offering the queen's pardon, on condition that they all returned to their allegiance; but Glencairn replied that they were not come there to seek pardon, but rather to give it those who had sinned; and Morton added, "We are not in arms against our queen, but the Duke of Orkney, the murderer of her husband, and are prepared to yield her our obedience, on condition that she dismisses him from her presence and delivers him up to us."