Aberdeen were unconvinced, but five hundred signatures were gathered in the town, as well as those of some fifty ministers of the district. The burgh of Dundee made him a burgess on the ground of his public services (28 May 1638; his name is given as ‘Henrysoune’ on the burgess ticket). After many ineffectual manœuvres, Charles convened a general assembly, which met at Glasgow on 21 Nov. 1638; on the 23rd Henderson was elected moderator, with no opposing vote except his own. At this critical meeting the prelates were condemned, and the presbyterian organisation of the Scottish church reconstituted on its existing lines. Hamilton, the royal commissioner, on the 28th took his leave of the assembly, declaring it to be dissolved. Proceedings were continued on the constitutional ground that the king's right to convene did not interfere with the church's independent right to hold assemblies. In his proclamation of 27 Feb. 1639, Charles treated the assembly's attitude as inimical to monarchy, and appealed to arms, reaching Berwick on 28 May. Henderson was one of the commissioners who arranged on 18 June the pacification of Berwick, after much personal discussion with Charles, who was satisfied of Henderson's loyalty, and spoke highly of his ability and prudence. The validity of the Glasgow assembly was left an open question, but its policy was confirmed, and Charles promised to convene an assembly yearly.
By this time Henderson had been promoted to an Edinburgh charge. On 4 May 1638 the town council elected him as one of the city ministers, but he was not released from Leuchars till 16 Dec. Dean Hannay was deposed from the charge of the high kirk on 1 Jan. 1639. Henderson was admitted on the 10th. At the Edinburgh assembly in August 1639 Henderson was again proposed as moderator; he declined, on the ground that the expedient of a permanent moderator had been a means of restoring episcopacy. David Dickson was elected, but Henderson was the ruling spirit. The assembly passed the first ‘Barrier Act,’ prohibiting new legislation till the motion had been approved by the consent of synods, presbyteries, and kirk sessions. The object was to prevent the court from obtaining a snatch vote in a thin assembly; but the reference to kirk sessions (repealed in the Barrier Act of 1697) is of importance as showing that, at this date, the Scottish presbyterians, like the English puritans, gave an independent voice to the church court of the individual congregation. Henderson preached before the parliament which met on 31 Aug., immediately after the close of the assembly, but was prorogued before it could ratify the assembly's acts.
In the following year he made himself unpopular in Edinburgh by his opposition to religious meetings, somewhat on the plan of the ‘prophesyings’ of the earlier puritans, which he regarded as promoting independent conventicles. At a conference in his house he brought over Dickson to his own view, and in June 1640 issued a series of caveats on the subject. Next month, at the Aberdeen assembly, in Henderson's absence, Henry Guthrie or Guthry [q. v.], afterwards bishop of Dunkeld, took exception to the issue of caveats as quasi-episcopal, but procured an act prohibiting private religious worship except in single families, and forbidding any but ministers and licentiates to ‘explain scripture.’
Meanwhile Henderson was with the covenanting army, which, crossing the border on 21 Aug., mastered Newcastle-on-Tyne and Durham before the end of the month. Disclaiming offensive war, the invaders petitioned the king to remove their national grievances. Commissioners on both sides met at Ripon on 1 Oct.; the conference was adjourned to Westminster. On 14 Nov. Henderson, who had fallen ill on the way, reached London, where the presence of the Scottish commissioners cemented the alliance of the covenanters with the party against Laud. While in London Henderson laid before Charles a plan for subsidising the Scottish universities from the bishops' rents. The office of rector of Edinburgh university had been revived in his favour (January 1640) by the town council, and he was annually re-elected till his death. His exertions in behalf of the education of his country, both in its colleges and parochial schools, were great and successful. He introduced at Edinburgh the teaching of Hebrew, and the system of honour classes known as ‘circles.’ For the colleges he secured a monopoly in the teaching of Greek and logic.
The treaty with the covenanters was not ratified till 7 Aug. 1641. It promised conformity of church government between the two kingdoms, by which Henderson understood a uniform presbyterianism; but Charles had taken care not to commit himself against a uniform episcopacy. Henderson had left London to attend the assembly at St. Andrews on 20 July. As he had not arrived, the assembly was adjourned to Edinburgh, where on 27 July he was elected moderator for the second time. On 28 July he carried a proposition for a confession of faith, a catechism, and a directory for worship. The object is
