On
19 August 1561 Queen Mary returned to Scotland and cannons were fired in Leith to announce her arrival. She celebrated Mass in the royal chapel at
Holyrood five days later and this prompted a protest. The next day she issued a proclamation that there would be no alteration in the current state of the religion and that her servants should not be molested or troubled. The effect of this was to maintain the
status quo of the law of religion within the country, but also to allow her to celebrate Mass within her household. Many in the nobility found this acceptable, but not to Knox. The following Sunday, he protested through the pulpit of St Giles'. This prompted Mary to summon Knox, just two weeks after her arrival. In this first exchange, Mary defended the
Church of Rome while Knox expounded on reformed doctrine. When Knox finished his sermon, he respectfully took his leave.
Before Christmas of that year, Mary approved an act that appropriated a quarter to a third of the ecclesiastical patrimony for the benefit of the nation which would include the support of the ministers of the Kirk. To Knox, this was insufficient and he continued to fight for a complete settlement of the issues as he had expounded in the Book of Discipline. He did this throughout 1562, but to no avail. The nobles were weary of his tirades. On
13 December, in an open denunciation, he gave a sermon that alluded to a comparison of the queen with Nero. Mary immediately summoned Knox again. This time it was more like a trial as her advisors, James Stewart, William Maitland, and
James Douglas were present. Knox explained the meaning of the sermon and asked if anyone present heard him say anything more than what he now presented. No one responded. Mary accepted the explanation and she stated that she did not blame Knox for the differences of opinion. She asked that he come to her directly if he heard anything about her that he disliked. Despite her friendly gesture, Knox simply insisted that he will continue to publically proclaim his differences in his sermons and that he will not wait upon her.
During Easter in 1563, some of the Roman priests celebrated Mass, thus defying the law. As the queen had done nothing on this matter, some Protestants tried to enforce the law themselves by apprehending some priests in
Ayrshire. This prompted Mary to summon Knox for the third time. She asked Knox to use his influence to promote religious toleration. He defended their actions using Biblical examples and noted she is bound to uphold the laws and if she did not, others would. She broke off the conversation, but the very next day, she surprised Knox by agreeing that the priests be brought to justice. She kept her word and on
19 May, 48 priests including the former
primate of Scotland were tried and placed in custody.
One week after this incident, Parliament met in the presence of Mary. Knox was expecting that Parliament would act on the Book of Discipline. He was told that nothing would be done because the Queen would soon be marrying and only afterwards would action be taken on the position of the Kirk. Maitland was trying to bring off a match between Mary and
Don Carlos. Knox lashed out against the proposed marriage in a sermon on
6 June. This drew protests even from Knox's friends and it led to one of the most dramatic interviews in Scottish history between the twenty-one-year old queen and John Knox. Shortly after Mary started to scold Knox, she burst into tears. "What have ye to do with my marriage? Or what are ye within this commonwealth?" she asked. "A subject born within the same, Madam," Knox replied. He noted that though he was not born of noble origins, he, as a member of the realm, is just as responsible to warn of dangers to the land if he foresees such dangers. Mary started to cry again to which Knox said, "Madam, in God's presence I speak: I never delighted in the weeping of any of God's creatures; yea I can scarcely well abide the tears of my own boys whom my own hand corrects, much less can I rejoice in your Majesty's weeping." Mary commanded him to leave thus ending the interview.
Knox's final encounter with Mary was prompted by an incident at Holyrood. While Mary was absent from Edinburgh, the Mass was still being celebrated in the chapel and a crowd forced their way in. During the altercation, the priest's life was threatened. Two of the ringleaders,
burgesses of Edinburgh were scheduled for trial on
24 October 1563. In order to defend these men, Knox sent out letters summoning the nobles to convene in order to discuss the matter. Mary obtained one of these letters and asked her advisors if this was not a treasonable act. The charge would be the unauthorised convocation of the queen's lieges. Stewart and Maitland did not want the incident to go to a public trial as they preferred to keep good relations with both the Kirk and the Queen. Knox was asked to admit he was wrong and to settle the matter quietly. He refused and he insisted on a public trial which took place a few days before Christmas. He defended himself in front of Mary and the nobles after which he was allowed to take his leave. The nobles were asked to vote on the charge against Knox and the result was unanimous. Knox was considered not guilty. Knox then presented himself before the
General Assembly of the Kirk on Christmas Day and asked whether he acted rightly or not. The General Assembly fully endorsed his actions.