Alexander Henderson (1586-1646) started his ministry in 1612 at Leuchars as a recipient of episcopal patronage but soon converted to the Presbyterian cause, opposing the articles of Perth at the general assembly of 1618. He remained at Leuchars despite attempts from larger churches to lure him away. He kept in touch with his non-conformist colleagues and came to the fore again in 1637, when he joined other clergy opposing the introduction of the new Scottish prayer book. He helped to form an organised opposition movement using petitions to complain that the book had been imposed without the authority of the general assembly, and that it encouraged Popish forms of worship. Together with Archibald Johnston of Wariston, he drew up the new national covenant. The first section of the document reproduced the 1581 king's confession, the second section summarized various acts of parliament against popery, and the third section was the new covenant proper. This was signed on 28 Feb 1638. He and Wariston spent the next few months preaching in favour of the covenant, writing tracts in support of holding a free general assembly and in negotiations with the kings commissioner, the marquis of Hamilton, to arrange the assembly, which finally began on 21 November. Henderson was elected moderator; he steered debate in favour of the covenanters despite objections from Hamilton. In December the assembly declared null the general assemblies of 1606 to 1616, abjured the five articles of Perth, denounced Arminianism, abolished episcopacy, and deposed the bishops.
After the general assembly Henderson moved from Leuchars to Edinburgh High Kirk and continued to support the covenanters through publishing tracts arguing the right of the Scottish people to defend their church against anyone seeking to break the covenant. A second general assembly was held in 1639 where Henderson declined the role of moderator but preached the opening sermon. He and Wariston again worked together to produce the solemn league and covenant in 1643, and was then appointed to lead the Scottish commissioners at the Westminster assembly and drafted the Westminster documents for them. The church soon fell into faction fighting after his death, showing the importance of his wise leadership while pursuing such a radical agenda.
The Church of Scotland grew out of the Catholic church at the Reformation in the 1560s, basing itself on Calvinist doctrine and practise to form a Presbyterian church. The following centuries saw numerous faction fights, splits and controversies over doctrine, organisation, whether or not to return to episcopacy, and control of the church by Royal and lay patrons. Struggles with Charles I and Charles II for control after the union of Scottish and English crowns in 1603 created the covenanters, following the signing of the national covenant in 1638, who were persecuted for their beliefs. The Revolution Settlement of 1690 finally established the Church of Scotland as the national church, the only Calvinist national church, but the peace did not last. The Secession Church of 1733 and the disruption of 1843 which saw a third of the church leave to form the Free Church of Scotland were only some of the divisions to split the church in later years. Many of the causes of the divisions had been addressed by the early 20th century to allow several of the main Presbyterian churches to regroup into a strong unified national church.