On 22 February 1638, in reply to a royal proclamation, he read a strong protestation to an enormous multitude assembled at the Mercat Cross in Edinburgh.

Together with Alexander Henderson he was the co-author of the National Covenant of 1638, drawing up the second part as a recapitulation of all the Acts of Parliament that had condemned "popery" while asserting the liberties of the Scottish church.

After Charles promised a new Assembly and Parliament to settle the church question, Johnston responded by accusing him of playing for time, to which the king replied in anger "that the devil himself could not make a more uncharitable construction or give a more bitter expression";[3] and on Johnston continuing his speech ordered him to be silent and declared he would speak to more reasonable men.

After the peace he continued to urge punishment of the incendiaries, especially of Traquair, and in a private interview with the king strongly opposed the proposed act of general oblivion.

[6] Lord Warriston was a chief agent in concluding the treaty with the English parliament in the autumn of 1643, and was appointed a member of the Committee of Both Kingdoms in London which directed the military operations, and in this capacity went on several missions to the parliamentary generals.

After the final defeat of Charles, when he had surrendered himself to the Scots, Johnston was made king's advocate in October 1646, and the same year was voted £3000 by the Scottish estates for his services.

He returned again after the Whiggamore Raid,[6] met Cromwell at Edinburgh in October after the defeat of the Engagers at Preston, and in conjunction with Argyll promoted the Act of Classes, passed on 23 January 1649, disqualifying royalists from holding public office.

After the defeat he urged the removal of General Leslie, afterwards Lord Newark, from the command of the Scottish army, and on 21 September delivered a violent speech in Charles' presence, attributing all the late misfortunes to the Stuarts and their opposition to the Reformation.

[6] After Dunbar the Committee of Estates persuaded the General Assembly of the Church of Scotland that it was necessary to abandon the Act of Classes to allow a new national army to be raised, to include supporters of the Engagement and other royalists.

The Act of Classes was duly abandoned, but the division between the majority Resolutioners and the minority Protestors was to haunt the Church of Scotland for decades after.

[7] Johnston lived in a mansion house at the foot of Warriston Close in Edinburgh (so named in his honour) on its east side, which had previously been home to Sir Lewis Craig.

He is described by his contemporary Robert Baillie as “one of the most faithful and diligent and able servants that our church and kingdom has had all the tymes of our troubles.”[7] He was learned in Scottish law, eloquent and deeply religious.

[7] Johnston had by nature no republican leanings; all the Royalists in Scotland, wrote Robert Baillie as late as 1646, could not have pleaded so much for the Crown and the King's just power as the Chancellor and Warriston did for many days together.

When, however, Presbyterianism was attacked and menaced by the Sovereign, he desired, like John Pym, to restrict the royal prerogative by a parliamentary constitution, and endeavoured to found his arguments on law and ancient precedents.

Johnston was wanting in tact and in consideration for his opponents, confessing himself that his natural temper (or rather distemper) "hath been hasty and passionate".