He had now been clerk to the general assembly since the year 1638, and when that unhappy difference fell out _anno_ 1650, when the act of classes was repeated, whereby malignants were again taken into places of power and trust; which occasioned the rise of those called protestors and resolutioners _anno_ 1650, lord Warriston was one of those who had a principal hand in managing affairs among those faithful anti-resolutioners; for he wrote a most solid letter to that meeting at St. Andrews, July 18, 1651, concerning which, the protestors, in their reasons, proving the said meeting to be no lawful, full or free general assembly, say, "Sir Archibald Johnston, clerk to the assembly a man undeniably faithful, singularly acquainted with the acts and proceedings of this kirk, and with the matters presently in controversy, and who hath been useful above many in all the tracts of the work of reformation, from the beginning, in all the steps thereof, both at home and abroad; having written his mind to the meeting (not being able to come himself) about the things that are to be agitated in the assembly, and held out much clear light from the scriptures, and from the acts of former assemblies, in these particulars. Albeit the letter was delivered publicly to the moderator, in the face of the assembly, and urged to be read by him who presented it, that then the moderator did break it up, and caused it to be read; and that many members did thereafter, upon several occasions, and at several diets, press the reading of it, but it could never be obtained, &c.[126]" And further, those papers bearing the name of representations, propositions, protestations, &c. were by the said lord Warriston, Messrs. Cant, Rutherford, Livingston, &c. presented to the reverend ministers and elders met at Edinburgh, July 24, 1652, when the marquis of Argyle at London procured an equal hearing to the protestors; and Mr. Simpson, one of these three ministers deposed by the assembly 1651, being sent up by the protestors for that purpose; in the beginning of 1657, Messrs. James Guthrie and Patrick Gillespie, the other three who had been deposed by that assembly, together with lord Warriston, were sent up to assist Mr. Simpson[127]. Lord Warriston had now, for the space of five years or more, wrestled and acted with all his power, for the king's interest, and, being a man of great resolution, he both spoke and wrote as openly against Scotsmen submitting to take offices under the usurper; but being sent up to London in the foresaid year 1657, with some of the Scots nobility, upon some important affairs, and Cromwel being fully sensible how much it would be for his interest to gain such a man as Warriston was, over to his side, he prevailed upon him to re-enter to the office of clerk-register; which was much lamented by this worthy man afterwards, as well as his sitting and presiding in some meeting at London after Oliver's death.