general assembly's committee for drafting a scheme of church government, which was set forth in the second ‘book of discipline,’ sanctioned by the general assembly (though not by the state) in 1581. His prominence as an ecclesiastical leader is shown by his being selected by the regent Morton in October 1577 as the first of three deputies to a proposed general council of protestants at Magdeburg. On 24 April 1578 he was for the first time elected moderator of the general assembly.
The second ‘book of discipline’ discarded every vestige of prelacy, set aside patronage, placed ordination in the hands of the eldership, and established a gradation of church courts. To church courts was assigned a jurisdiction independent of the civil magistrate. On the one hand, the exercise of civil jurisdiction was forbidden to the clergy; on the other, the church court was entitled to instruct the civil magistrate in the exercise of his jurisdiction, according to the divine word. It did not, however, complete the development of the Scottish ‘presbytery,’ for it recognised no intermediate court between the eldership of the particular congregation and the assembly of the province; though it pointed the way to ‘presbyteries’ by allowing three or four contiguous congregations to have an eldership in common. Melvill's ecclesiastical polity has been treated as the fruit of his experience of foreign protestantism, especially in Geneva. As regards his grasp of principles this is true. But he did not bring with him from abroad any rigid model to be followed, and the ultimate shape of Scottish presbyterianism was a native growth.
Melvill's ideas of Scottish university reform were not limited to Glasgow. In 1575 he assisted Alexander Arbuthnot (1538–1583) [q. v.], principal of King's College, Aberdeen, in the formation of a new constitution for that university. In 1578 he was appointed by the Scottish parliament a commissioner for the visitation of St. Andrews, the richest and most frequented of the Scottish universities. The plan for its reformation (ratified 11 Nov. 1579) was mainly his; he had the advantage here of working on the lines of a prior scheme drawn up in 1563 by George Buchanan (1506–1582) [q. v.], on which, however, he materially improved. Of the three colleges at St. Andrews, St. Mary's, or the New College (begun 1532, finished 1552), was henceforth reserved for a four years' course of theological studies under five professors.
In October 1580 a royal letter invited the concurrence of the assembly in the translation of Melvill to St. Andrews as principal of St. Mary's. Melvill accepted the appointment in November. Chairs at St. Andrews were at once offered, but in vain, to Thomas Cartwright (1535–1603) [q. v.] and Walter Travers (see letter in Fuller, Church Hist. bk. ix. p. 215; internal evidence proves the date). Taking with him his nephew James as professor of oriental languages, Melvill began his work at St. Andrews in December 1580. The new arrangements had displaced several men who had grievances not easily satisfied. The professors of St. Leonard's College delivered inflammatory lectures in fierce defence of the authority of Aristotle, ‘owirharled’ by Melvill in the name of the new learning. In return he promoted the real study of Aristotle, created a taste for Greek letters, and in philosophy, as in biblical knowledge, superseded the second-hand methods of an effete scholasticism. In September 1581 he paid a visit in Edinburgh with other friends to George Buchanan, whose history was then in the press. Buchanan showed them the epistle dedicatory to the king, which Melvill thought ‘obscure in sum places.’ Buchanan seems to have accepted Melvill's corrections.
At the general assembly which met at Edinburgh in October 1581, Melvill exhibited fifteen articles of libel against Robert Montgomery (d. 1609) [q. v.], who had accepted from Esmé Stuart, first duke of Lennox [q. v.], the see of Glasgow, the revenues, except a small pension, going to Lennox himself. It was this kind of simoniacal arrangement which gave rise to the name of ‘tulchan’ bishops. The prosecution of Montgomery was resumed at the general assembly which met at St. Andrews, in St. Mary's College, on 24 April 1582, Melvill being moderator. In the face of a royal inhibition, Montgomery was tried, convicted on eight articles, and would have been excommunicated but for his temporary submission. As the submission did not last, the assembly's order for excommunication was carried out by John Davidson (1549?–1603) [q. v.] at Liberton, near Edinburgh. The assembly and the court were now at open war. A special meeting of assembly was convened at Edinburgh on 27 June. Melvill, in his opening sermon, denounced the doctrine of the ecclesiastical supremacy of the crown. He was retained as moderator, and appointed on a commission to wait upon James VI at Perth with a remonstrance and petition. His relatives urged the danger of his errand, but Melvill was fearless. He presented the remonstrance to the king in council. ‘Wha,’ exclaimed Arran, ‘dar subscryve thir treasonable articles?’ Melvill replied, ‘We dar and will,’ and immediately subscribed, followed by the other commissioners.