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 appointed on the 13th of November 1641 a lord of session, with the title of Lord Warriston (a name derived from an estate purchased by him near Edinburgh in 1636), was knighted, and was given a pension of £200 a year. The same month he was appointed a commissioner at Westminster by the parliament for settling the affairs of Scotland. He 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. He took his seat early in 1644 in the Assembly of Divines, to which he had been nominated, and vehemently opposed measures tolerating independency or giving powers to laymen in ecclesiastical affairs. The articles of the unsuccessful treaty of Uxbridge were, for the most part, drawn up by him the same year. Besides his public duties in England he sat in the Scottish parliament for the county of Edinburgh from 1643 till 1647, was speaker of the barons, and served on various committees. After the final defeat of Charles, when he had surrendered himself to the Scots, Johnston was made in October 1646 king’s advocate, and the same year was voted 3000 by the estates for his services. He continued to oppose unwise concessions to Charles, and strongly disapproved of the “engagement” concluded in 1648 by the predominant party with Charles at Carisbrooke, which, while securing little for Presbyterianism, committed the Scots to hostilities with the followers of Cromwell. He now became the leader of the “remonstrants,” the party opposed to the “engagement,” and during the ascendancy of the engagers retired to Cantyre as the guest of Argyll. He returned again after the Whiggamore Raid, 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 the 23rd of January 1649, disqualifying the royalists. The good relations now farmed with Cromwell, however, were soon broken off by the king’s execution, and Johnston was present officially at the proclamation of Charles II. as king at Edinburgh, on the 5th of February 1649. On the 10th of March he was appointed lord clerk register. In May he pronounced the vindictive sentence on Montrose, and he is said to have witnessed with Argyll the victim being drawn to the place of execution. He was present at the battle of Dunbar (3rd of September 1650) as a member of the committee of estates, to which body is ascribed the responsibility for Leslie’s fatal abandonment of his position on Doon Hill. After the defeat he urged the removal of David Leslie, afterwards Lord Newark, from the command, and on the 21st of September delivered a violent speech in Charles’s presence, attributing all the late misfortunes to the Stuarts and to their opposition to the Reformation.

His first object in life being the defence of Presbyterianism, Johnston could join neither of the two great parties, and now committed himself to the faction of the remonstrants who desired to exclude the king, in opposition to the resolutioners who accepted Charles. The latter for some time maintained their superiority in the kingdom, Johnston being reduced to poverty and neglect. In the autumn of 1656 Johnston went to London as representative of the remonstrants; and soon afterwards, on the 9th of July 1657, he was restored by Cromwell to his office of lord clerk register, and on the 3rd of November was appointed a commissioner for the administration of justice in Scotland, henceforth remaining a member of the government till the Restoration. In January 1658 he was included by Cromwell in his new House of Lords, and sat also in the upper chamber in Richard Cromwell’s parliament. On the latter’s abdication and the restoration of the Rump, he was chosen a member of the council of state, and continued in the administration as a member of the committee of public safety, maintaining consistently his attitude against religious toleration. At the Restoration he was singled out for punishment. He avoided capture, escaping to Holland and thence to Germany, and was condemned to death in his absence on the 13th of May 1661. In 1663, having ventured into France, he was discovered at Rouen, and with the consent of Louis XIV. was brought over and imprisoned in the Tower of London. In June he was taken to Edinburgh and confined in the Tolbooth. He was hanged on the 22nd of July at the Market Cross, Edinburgh, the scene of many of his triumphs, and a few yards from his own house in High Street, which stood on the east side of what is now known as Warriston’s Close. His head was exposed on the Netherbow and afterwards buried with his body in Greyfriars churchyard.

Johnston was a man of great energy, industry and ability, and the successful defence of their religion by the Scots was probably owing to him more than to any other man. 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.” He was learned in the Scottish law, eloquent and deeply religious. His passionate devotion to the cause of the Scottish church amounted almost to fanaticism. According to the History by his nephew Bishop Burnet, “he looked on the Covenant as the setting Christ on his throne.” He had by nature no republican leanings; “all the Royalists in Scotland,” writes 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 Pym, to restrict the royal prerogative by a parliamentary constitution, and endeavoured to found his arguments on law and ancient precedents. His acceptance of office under Cromwell hardly deserves the severe censure it has received. He stood nearer both in politics and religion to Cromwell than to the royalists, and was able in office to serve usefully the state and the church, but his own scrupulous conscience caused him to condemn in his dying speech, as a betrayal of the cause of Presbyterianism, an act which he regarded as a moral fault committed in order to provide for his numerous family, and the remembrance of which disturbed his last hours. 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.” He was hated by Charles I., whose statecraft was vanquished by his inflexible purpose, and by Charles II., whom he rebuked for his dissolute conduct; but he was beloved by Baillie, associated in private friendship and public life with Argyll, and lamented by the nation whose cause he had championed.

He had a large family, the most famous of his sons being James Johnston (1655–1737), called “secretary Johnston.” Having taken refuge in Holland after his father’s execution, Johnston crossed over to England in the interests of William of Orange just before the revolution of 1688. In 1692 he was appointed one of the secretaries for Scotland, but he was dismissed from office in 1696. Under Anne, however, he began again to take part in public affairs, and was made lord clerk register. Johnston’s later years were passed mainly at his residence, Orleans House, Twickenham, and he died at Bath in May 1737.

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