Mary, according to Knox, was exciting the Duke against Argyll and Lord James, by the charge that Lord James was aiming at the crown, in which if he succeeded, he would deprive not only her daughter of the sovereignty, but the Hamiltons of the succession.

Young and ambitious as Lord James then was, and heavily as he was suspected, even in England, it is most improbable that he ever thought of being king.
The Congregation refused to let Argyll and Lord James hold conference with the Regent.

Other discussions led to no result, except waste of time, to the Regent's advantage; and, on July 22, Mary, in council with Lord Erskine, Huntly, and the Duke, resolved to march against the Reformers at Edinburgh, who had no time to call in their scattered levies in the West, Angus, and Fife.

Logan of Restalrig, lately an ally of the godly, surrendered Leith, over which he was the superior, to d'Oysel; and the Congregation decided to accept a truce (July 23-24).
At this point Knox's narrative becomes so embroiled that it reminds one of nothing so much as of Claude Nau's attempts to glide past an awkward point in the history of his employer, Mary Stuart.

I have puzzled over Knox's narrative again and again, and hope that I have disentangled the knotted and slippery thread.
It is not wonderful that the brethren made terms, for the "Historie" states that their force numbered but 1500 men, whereas d'Oysel and the Duke led twice that number, horse and foot.