A memorable meeting of the General Assembly was held in August 1643. Henderson was elected moderator for the third time. He presented a draft of the famous "Solemn League and Covenant," which was received with great enthusiasm. Unlike the "National Covenant" of 1638, which applied to Scotland only, this document was common to the two kingdoms. Henderson, Baillie, Rutherford and others were sent up to London to represent Scotland in the Assembly at Westminster. The "Solemn League and Covenant," which pledged both countries to the extirpation of prelacy, leaving further decision as to church government to be decided by the "example of the best reformed churches," after undergoing some slight alterations, passed the two Houses of Parliament and the Westminster Assembly, and thus became law for the two kingdoms. By means of it Henderson has had considerable influence on the history of Great Britain. As Scottish commissioner to the Westminster Assembly, he was in England from August 1643 till August 1646; his principal work was the drafting of the directory for public worship. Early in 1645 Henderson was sent to Uxbridge to aid the commissioners of the two parliaments in negotiating with the king; but nothing came of the conference. In 1646 the king joined the Scottish army; and, after retiring with them to Newcastle, he sent for Henderson, and discussed with him the two systems of church government in a number of papers. Meanwhile Henderson was failing in health. He sailed to Scotland, and eight days after his arrival died, on the 19th of August 1646. He was buried in Greyfriars churchyard, Edinburgh; and his death was the occasion of national mourning in Scotland. On the 7th of August Baillie had written that he had heard that Henderson was dying "most of heartbreak." A document was published in London purporting to be a "Declaration of Mr Alexander Henderson made upon his Death-bed"; and, although this paper was disowned, denounced and shown to be false in the General Assembly of August 1648, the document was used by Clarendon as giving the impression that Henderson had recanted. Its foundation was probably certain expressions lamenting Scottish interference in English affairs.