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 generals (Cal. State Papers, Dom. 1644–5, passim).

While Charles was a virtual prisoner with the Scots at Newcastle he made Johnston, 30 Oct. 1646, king's advocate, an office equivalent to that of the modern lord advocate. The appointment was ratified by the Scottish parliament. In the same year the estates voted him 3,000l., ‘because he had expended himself and his purse’ (Scotch Acts, vol. vi. pt. ii. p. 772). In 1648 the king's party in the Scottish parliament triumphed, and formed the famous ‘engagement’ to support Charles, then a prisoner at Carisbrook. It was vehemently resisted by Johnston. The committee of estates which had sanctioned the ‘engagement’ was dispersed after the battle of Preston, and in a new parliament from which ‘engagers’ were excluded Johnston took his seat as commissioner for Argyllshire. By this parliament was passed, 23 Jan. 1649, the Act of Classes, imposing disqualifications upon all ‘engagers’ and their friends. Johnston zealously supported, and is supposed to have framed, the Act. Although never friendly to the royal cause, Johnston was present officially when Charles II was proclaimed king at Edinburgh, 5 Feb. 1649 (ib. vol. vii. pt. ii. p. 178). He was appointed (10 March 1649) lord clerk register, and as such became the custodian of the Scottish records. He is said to have opposed the despatch of commissioners to Charles II, and the invitation to the young king to come to Scotland on certain conditions (, iii. 416, iv. 2). Yet he is also said to have drawn up the treaty of Breda, which brought Charles II to Scotland (, Life, p. 331). Johnston was one of the members of the committee of estates who were with David Lesley and the Scottish army before and at the battle of Dunbar. His nephew, Bishop Burnet (i. 74–5), makes him one of the persons responsible for Lesley's fatal abandonment before the battle of his strong position on Doon Hill, which Baillie (iii. 1), without mentioning Johnston, represents as made against Lesley's own wish by order of the committee of estates (cf., Letters and Speeches of Cromwell, iii. 34).

After the battle of Dunbar (3 Sept. 1650) Johnston is said to have had several interviews with Cromwell (, iv. 2). They corresponded about the Scottish records which fell into the hands of the English (, Cromwell, iii. 127–8). Johnston was now in a very perplexing situation. His presbyterianism hindered an alliance with Cromwell, and made him equally hostile to Prince Charles, whom he is said to have irrevocably offended by lecturing him upon his looseness of morals (see, p. 173). He was drawn towards the independent section, who, while resisting Cromwell, doubted Charles, and called for the expulsion of all ‘malignants’ from the army. Johnston was present at Dumfries when the remonstrance embodying the independent section's complaints was drawn up (, iii. 118), and in the committee of the estates, in the presence of the king, he admitted that he had been ‘at the voting of it,’ though he had ‘refused to give his vote therein’ (, iii. 169). The feud between the ‘remonstrants’ (those who with Johnston supported the remonstrance) and the ‘resolutioners’ (those who had passed resolutions in the parliament and assembly against the remonstrance) lasted after the English rule had been established in Scotland. With the new rule Johnston lost his offices, and seems to have been reduced to poverty.

In 1652 Johnston signed and probably composed a protest against the subordination, under English rule, of kirk to state in spiritual matters (, 6 Feb. 1652). In 1653 Whitelocke reports (7 June, p. 557) tidings from Scotland that ‘the Lord Warriston is angry at everything but himself, and at that too sometimes.’ In 1654 Baillie (iii. 249) speaks of him as generally hated and neglected. In 1655 his action and that of James Guthrie [q. v.] made a conference between the two parties abortive. In 1656 Lord Broghill, president of the council of state at Edinburgh, writes to the Protector of Johnston and Guthrie as ‘Fifth-monarchy presbyterians’ (Scotch Acts, vol. vii. pt. ii. p. 899;, iv. 557).

The resolutioners and remonstrants at last appealed to Cromwell. Johnston became one of the commissioners on the part of the remonstrants to proceed to London, reluctantly, according to Wodrow (i. 361), because he justly feared his own weakness. He finally accepted on 9 July 1657 his old office of lord clerk register from Cromwell, who naturally favoured the remonstrants, and one of his first acts after his reappointment was to procure the restoration to Scotland of such Scottish records as related to private matters (Cal. State Papers, Dom. 1657–8, pp. 37, 182). Cromwell also made him, 3 Nov. 1657, one of the commissioners for the administration of justice in Scotland, and called him to his House of Peers (January 1658), where he is said to have been a frequent speaker (, i. 1667). He was also summoned to Richard Cromwell's House of Peers. On the restoration of the Rump he was one of those chosen by ballot to form a new council of state, over which he frequently presided. On the sup-