When Holyrood had been invaded by a mob who, in Mary's absence in autumn 1563, broke up the Catholic attendants on Mass (such attendance, in Mary's absence, was illegal), and when both parties were summoned to trial, Knox called together the godly.

The Council cleared him of the charge of making an unlawful convocation (they might want to make one, any day, themselves), and he was supported by the General Assembly.

Similar conduct of the preachers thirty years later gave James VI.

the opportunity to triumph over the Kirk.
In June 1564 there was still discord between the Kirk and the Lords, and, in a long argument with Lethington, Knox maintained the right of the godly to imitate the slayings of idolaters by Phineas and Jehu: the doctrine bore blood-red fruits among the later Covenanters.

Elizabeth, in May 1564, in vain asked Mary to withdraw the permission (previously asked for by her) to allow Lennox to visit Scotland and plead for the restitution of his lands.