Armed with his new provisions, the King immediately began to use them with energy. Edinburgh and St. Andrews were the strongholds of the Church, where the Invincibles in its ministry were chiefly found. The ministers of the former had already been disposed of, and the King's next move was directed against those of the latter—above all, against Melville, the chief Invincible. The two leading ministers of St. Andrews, Black and Wallace, were discharged; George Gledstanes, who afterwards became a Bishop, being appointed in Black's place; and Melville was deprived of the Rectorship of the University. At the same time, a law was enacted depriving professors of their seats in Church Courts, the object being, of course, to exclude Melville, whose influence in the Courts was so commanding.

At the end of this year another step was taken towards the re-erection of Episcopacy. The Commissioners of Assembly, who were now mere creatures of the King, appeared before Parliament, petitioning it to give the Church the right of representation, so as to restore it to its former position as the Third Estate of the realm; proposing also, that for this end the prelatic order should be revived, and the Bishops chosen as the Church's representatives. The jurisdiction of the prelates within the Church was to be left over for future consideration, in accordance with James's policy, which was not to filch so much of the Church's liberty at any one time as might frustrate his hope of taking it all away in the end. The petition of the Commissioners was granted by the Parliament.

In February of the following year, 1598, the Synod of Fife met, Sir Patrick Murray being present as the King's Commissioner; and the Court at once entered on the question of the hour, Should the Church agree to send representatives to Parliament? James Melville, who was the first to rise and address the House, protested against their falling to work to 'big up' bishops, whom all their days they had been 'dinging doun.' Andrew Melville followed, and supported his nephew's counsel in his own vehement manner. David Ferguson, the oldest minister of the Church, who had been at its planting in 1560, rose and warned the House of the fatal gift that was offered by the King. John Davidson, another venerable and influential member of the Synod, made a powerful speech, concluding with the same warning: 'Busk, busk, busk him as bonnilie as ye can, and fetche him in als fearlie as yie will, we sie him weill aneuche, we sie the horns of his mytre.' When the Synod met, the majority were inclined to favour the proposal; but these speeches, greatly to the chagrin of the Royal Commissioner, turned the feeling of the House.

The same business occupied the next Assembly, which met in Dundee in March. Melville having come to the Assembly in defiance of the recent Act depriving him of his seat, the King challenged his commission in the Court. Melville replied with great spirit; and before he was discharged, delivered his views on the King's policy. John Davidson boldly defended his leader's right to sit in the Assembly, and, turning to the King, told him that he had his seat there as a Christian man, and not as President of the Court. Next day Davidson complained again of the treatment Melville had received, openly ascribing it to the King's fear of his opposition. 'I will not hear a word on that head,' James burst forth.—'Then,' said Davidson, 'we must crave help of Him that will hear us.' Not only was Melville excluded from the Assembly, but its business was not allowed to proceed till he left the town, lest he should stiffen the brethren who resorted to him for advice against the King's proposals. The royal measures were, after all, only carried by ten votes; and even that majority would not have been secured had the King not declared, with his usual disingenuousness, that he had no intention of restoring the bishops as a spiritual order, but only as representatives of the Church in Parliament.

It was decided that the number of representatives should correspond with that of the old prelates, and that they should be chosen conjointly by the King and the Assembly. When, however, the House proceeded to details, so much difference of opinion arose, that the King thought it prudent to adjourn. The questions were referred to the inferior Courts for their consideration, and thereafter each Synod was to appoint three commissioners to confer on the subject before the King along with all the theological professors.

This conference was held, and was packed with the King's men. In many cases the delegates were not the choice of those they represented. The trick by which this was effected was in keeping with the rest of the King's conduct in the business. In many of the presbyteries the Invincibles were placed upon the leets from which the commissioners were to be elected; they thus lost their votes, and those who remained to make the choice chose the delegates desired by the King.

Melville attended the conference, and opposed the King at every point. On the question of the duration of the office of the representatives, there was a very lively piece of repartee between the two. Melville had been contending that the King's proposal to appoint the representatives for life would establish lordship over the brethren, 'tyme strynthning opinioun and custome confirming conceat,' when the King broke in upon his speech with the remark that 'there was na thing sa guid bot might be bathe ill suspected and abbusit, and sa we suld be content with na thing.' Melville retorted that they 'doubted of the guidness, and had ower just cause to suspect the evill of it.' The King's next thrust was: 'There was na fault bot we [the ministers] war all trew aneuche to the craft,' which Melville turned with the remark, 'But God make us all trew aneuche to Christ say we.'—'The ministers,' said the King, 'sould ly in contempt and povertie [if their status was not raised as he proposed].—'It was their Maister's case before them,' rejoined Melville; 'it may serve them weill aneuche to be as he was, and better povertie with sinceritie nor promotioun with corruptioun.'—'Uthers would be promovit to that room in Parliament,' said the King [his Majesty could not want his three estates], 'wha wald opres and wrak his Kirk.'—Melville answered: 'Let Chryst the King and advenger of the wrangs done to his Kirk and them deal togidder as he hes done before; let see wha gettes the warst.'—Once more the King argued: 'Men wald be that way [by a temporary appointment] disgraced, now sett upe and now sett by and cast down and sa discouragit from doing guid,' when Melville concluded: 'He that thinks it disgrace to be employed in what God's Kirk thinks guid, hes lytle grace in him; for grace is given to the lowlie.'

Another point was the name to be given to the representatives. Arguing against the King's proposal to style them bishops, Melville used great freedom of speech: 'The nam επισκοπος being a Scripture nam, might be giffen tham, provyding, that because ther was sum thing mair put to the mater of a Bischope's office then the Word of God could permit, it sould have a lytle eik[23] put to the nam quhilk the Word of God joyned to it, and sa it war best to baptize tham with the nam that Peter i. cap. iv. giffes to sic lyk officers, calling tham αλλοτριοεπισκοπους, war nocht they wald think scham to be merschallit with sic as Peter speakes of ther, viz., murderers, theiffs, and malefactors?' Melville was much pleased with his own wit: 'Verilie that gossop [this was Andro] at the baptisme (gif sa that I dar play with that word) was no a little vokie[24] for getting of the bern's name,' We hardly understand Melville unless we take into account the spirit almost of glee with which he fought 'the good fight'; he was 'always a fighter,' not purely from stress of circumstances, but because he had it in him; he was never quarrelsome, and he needed a high issue to rouse him—but that given, he sniffed the battle from far, and dearly loved to be in the thick of it.

The questions were then left to be disposed of by the General Assembly, the King warning the members of the conference before it broke up that, whatever the Assembly might do, he would have his Third Estate restored.

By this time the country had learned, by the publication of the King's two books—The True Law of Free Monarchy and the Basilicon Doron—that James's practice in the government of the nation and in his policy towards the Church was in accordance with his theory of kingship. By a 'Free Monarchy' he meant, not a monarchy in which the people are free, but in which the King is free from all control of the people. He claimed that the King was above the law; and that 'as it is atheism and blasphemy to dispute what God can do, so it is presumption and a high contempt in a subject to dispute what a King can do, or to say that a King cannot do this or that.'