made plain in his official reply to a letter, received 9 Aug., from London divines; he there pleads, in the assembly's name, that the same formularies should be binding on both kingdoms. The duty of drafting these formularies was put upon Henderson by the assembly. His other occupations stood in the way; moreover, he saw the necessity of co-operation with England. ‘We are not to conceive,’ he wrote to Baillie, on 20 April 1642, ‘that they will embrace our form. A new form must be set down for us all.’ Pleading his health, which always suffered in Edinburgh, and the weakness of his voice, he asked to be transferred to a country charge. He declined the principalship of St. Andrews, and was released from active duty, but was persuaded to remain in Edinburgh. On Sunday, 15 Aug., the day after the arrival of Charles at Holyrood, Henderson preached before him. His remonstrance, when the king went to golf instead of to afternoon service, was taken in good part; he was made royal chaplain, with the rents of the deanery of the Chapel Royal, and was in close attendance on Charles, who for the moment conceded all the covenanters' demands.
The favours Henderson received from Charles, and the moderation of his sermons, gave offence to the more rigid covenanters. He was not sent with the new commissioners to London in 1642, and in the St. Andrews assembly in July he was openly accused of temporising. He usually sat silent under misconstructions (Baillie), but on this occasion he made a ‘passionate vindication of his conduct’ (Aiton). The assembly appointed him to frame their answer to a communication from the English parliament; in doing so, he urged his proposal for an ecclesiastical uniformity. The reply of the English parliament (received 21 Sept.) invited the assembly to send deputies to an assembly of divines in England by 5 Nov. The civil war had now broken out, and the project was delayed.
At this crisis Henderson exercised all his diplomacy in the interests of neutrality. His suggestion that the queen should come from Holland to Scotland as a mediator was distrusted by Charles. Empowered by the council and the commission of assembly, Henderson, with Loudon, was despatched to Oxford at the end of February 1643, to urge on the king the calling of a parliament in Scotland as the only means of preserving loyalty. The negotiation was fruitless, though protracted till the beginning of May, when Henderson returned to Scotland, having declined a disputation on episcopacy with the Oxford divines. Equally fruitless was his conference with Montrose at the bridge of Stirling.
The invitation to an assembly of divines was renewed by English commissioners (Sir Harry Vane the younger, Stephen Marshall, and Philip Nye) to the Edinburgh assembly in August 1643, when Henderson was moderator for the third time. The Westminster assembly, already in session, having been convened by ordinance of 12 June, added its formal request to the missive of the English parliament. Private conferences were held with members of the Scottish convention of estates as to the terms on which the assembly's delegates were to go to England. It was at length decided to enter into a league with the English parliament. The English commissioners were for a purely civil engagement; their Scottish allies insisted on a religious bond. Drafted by Henderson, the ‘solemn league [Vane added this word] and covenant’ was introduced to the assembly on 17 Aug. and unanimously adopted. It is an instrument of impressive power and singular skill, vowing the extirpation of prelacy, but leaving the further question to be determined by ‘the example of the best reformed churches.’ With a definition of prelacy, introduced to meet the scruples of Cornelius Burges [q. v.], it was accepted by the general body of puritans throughout the three kingdoms. At the taking of the ‘league and covenant’ by the Westminster assembly on 25 Sept. at St. Margaret's, Henderson delivered an oration on the good effects of previous covenants in Scotland.
The growing influence of the independents, with whom, but for the advice of Baillie, he would have come to an open rupture, marred his endeavours for uniformity. Henderson's work in the Westminster assembly was chiefly that of drafting the directory for worship. With his scheme of uniformity was connected, according to Aiton, the plan of an authorised psalm-book, the metrical version by Sir Francis Rous being taken as the basis. He would have had the assembly sit on Christmas day, and succeeded in getting parliament to keep a solemn fast at this season (Wednesday, 27 Dec. 1643), when he preached before the commons.
To the Uxbridge conference, opened 30 Jan. 1645, Henderson was commissioned both by the Scottish assembly and the English parliamentary committee as a manager of the proposed religious settlement. On leaving Uxbridge he obtained a passport for Holland, but appears to have remained in London. He thought of returning to Scotland in October, but sent Baillie in his stead.