The Covenanters therefore determined to hold together and be prepared. On the 22nd of September, 1638, the Marquis of Hamilton caused the royal proclamation to be read at the market-cross at Edinburgh, abandoning the Anglican Service and the High Commission Court; but as it required subscription to the old confession of faith, there was no rejoicing on the occasion. There were two particulars in this proclamation which fully justified the Scots in refusing to comply with it. It stated that the vow of the Covenant was unauthorised by Government, and therefore illegal; and it professed to grant a pardon for that act to all who signed the confession, which would have acknowledged that the nation had been guilty of a crime in accepting the Covenant, a thing they were not likely to admit, for in that case they could not have refused the re-admission of the very liturgy against which they were at war. They therefore published a protest against the proclamation, founded on these reasons.

The marquis having obtained the signature of the Lords of the Secret Council to the new bond, which Charles had previously signed, though it contained many clauses repugnant to Arminianism, issued the proclamation for the meeting of the Assembly in Glasgow on the 21st of November, 1638, and for that of the Parliament on the 17th of May, 1639. In a few days afterwards, the Council published an act discharging the Book of Common Prayer, the Book of Canons, etc., and called for the subscription of all his Majesty's subjects. The municipal bodies, the ministers, and the people hastened to thank the Council, and to express their joy at the revocation of the obnoxious orders, but they refused to sign the confession.

The marquis wrote to Charles, informing him of the determined spirit of the people, and advising him to hasten his military preparations. He also represented to him the protests of the bishops against the holding of the Assembly; but the king bade him persist in holding it, so that he might not appear to break faith with the public and thus precipitate matters, but to counteract the effect of the Assembly by sowing discord amongst the members, and protesting against their tumultuary proceedings.

But the Scots did not give Hamilton much time for such machinations before the meeting of the Assembly. They were warned by a trusty correspondent—notwithstanding the waylaying of the post was carried into effect—that vigorous preparations were being made to invade Scotland. There were arms for twenty thousand men, including forty pieces of ordnance and forty carriages; but the writer did not believe they would get two hundred men for the service, such was the desire of all parties—nobles, gentry, and people—for their success, which if obtained, he said, would lead many of all ranks to settle in Scotland for freedom of conscience. He added that Wentworth had made large offers of assistance to the king from Ireland, but that the Irish were themselves so injured that he doubted whether any considerable help would be had from Wentworth against them; yet if Charles could muster sufficient force, they might expect no terms from him but such as they would get at the cannon's mouth.

At the end of October the Earl of Rothes demanded from Hamilton a warrant citing the bishops as guilty of heresy, perjury, simony, and gross immorality, to appear before the approaching Assembly. The marquis refused, on which the Presbytery of Edinburgh cited them. Charles had ordered, as a sign of his favour, the restoration of the Lords of Session of Edinburgh, but on condition of their signing the confession of faith. Nine out of the fifteen were induced with much difficulty to sign, but from that moment they were in terror of their lives from the exasperation of the people.

When Hamilton arrived on the 17th of November in Glasgow to open the Assembly, he found the town thronged with people from all quarters, evidently in intense excitement. The Tables had secured the most popular elections of representatives to the Assembly, sending one lay elder and four lay assessors from every Presbytery. The marquis therefore found himself overruled on all points. In his opening speech he read them the king's letter, in which Charles complained of having been misrepresented, as though he desired innovations in laws and religion; and to prove how groundless this was, he had granted this free Assembly, for settling all such matters to the satisfaction of his good subjects. He then of himself protested against the foul and devilish calumnies against his sacred Majesty, purporting that even this grant of the Assembly was but to gain time whilst he was preparing arms to force on the nation the abhorred ritual. The marquis, whilst he was making these solemn asseverations, being well assured, as were most of his hearers, that the king was all the while casting cannon and ball, and mustering soldiers for this "foul and devilish purpose," the Assembly must have been perfectly satisfied that no good was to be expected but from their own firmness. They at once proceeded to elect Alexander Henderson as their Moderator, and Hamilton protested as vigorously against it, but in vain. They next elected as clerk-register Archibald Johnstone, the clerk of the Edinburgh Tables, against which Hamilton again protested with as little effect, Johnstone declaring that he would do his best to "defend the prerogative of the Son of God."

Defeated on these important points, the marquis the next day entered a protest against the return of lay members to the Assembly; and the proctor on behalf of the bishops added their protest, declining the authority of the Assembly, which he contended ought to be purely ecclesiastical. James had, in fact, put the lay members out of the Assembly, and the king therefore treated this original constitution of the Assembly, as settled at the Reformation, as an innovation, turning the charge of innovation on the Covenanters. The marquis would then have read the protests of the bishops with which he was furnished; but the Assembly declined to hear them, and repeated that they would pursue the charges against the bishops so long as they had lives and fortunes. On this Hamilton dissolved the Assembly, and the same day wrote a most remarkable letter to Charles, which appears to leave little ground for the suspicions of the royal party that he was secretly inclined to the Covenant. He informed the king that he had done his utmost, but to no purpose, with that rebellious nation. He seemed to apprehend danger to his life, and that this might be the last letter he should ever write to his Majesty. He blamed the bishops for persuading the king to bring in the English liturgy and canons in so abrupt and violent a manner; that their pride was great, their folly greater. He gives the king his opinion of the character and degrees of the trustworthiness of the different Ministers, and bids him beware of the Earl of Argyle, whom he declares to be the most dangerous man in the State; so far from favouring episcopacy, as had been supposed, that nobleman wished it abolished with all his soul. This was immediately afterwards, as we shall see, made clear by Argyle himself. Hamilton then proceeded to instruct the king how best to proceed to quell what he deemed not merely a contest for religion, but an incipient rebellion. It was to blockade the ports, and thus cut off all trade, by which the burghs, the chief seats of the agitation, lived. As fast as these burghs felt their folly and returned to their allegiance, they should be restored to favour, and their ports opened, which would make the rest anxious to follow. He said he had done his best to garrison the castle of Edinburgh, though it was in a precarious state, but that the castle of Dumbarton might be readily garrisoned by troops from Ireland. If he preserved his life, which he seemed to doubt, he would defend his post to the utmost, though "he hated the place like hell," and as soon as he was free of it would forswear the country. He recommended his brother to the king's favour and his children to his protection if they lived; and to these, if they did not prove loyal, he left his curse. His daughters, he desired, might never marry into Scotland.

The marquis clearly saw the dreadful conflict which was approaching, and his tears and emotion on dismissing the Assembly struck every one with that impression. But the Assembly had no intention of dispersing. Like the Commons of England, they entertained too high an estimate of their right, and of their duty in such a crisis. They therefore passed a resolution declaring the Kirk independent of the civil powers, and the dissolution of the Assembly by the Royal Commissioner illegal and void. They said that if the Commissioner should see fit to quit the country, and leave the Church and kingdom in that disorder, it was their duty to sit; and that they would continue to sit till they had settled all the evils which came within their lawful and undoubted jurisdiction.

Laud, in reply to Hamilton, lamented that fear of giving umbrage to the Covenanters too soon had too long delayed the means to crush them. He thanked him for having conveyed the bishops to Hamilton Castle to protect them, and trusted that his own life would yet be preserved from the diabolical fury of the Scots. What Hamilton had foreseen in the meantime had come to pass. The Earl of Argyle declared plainly in the Council that he would take the Covenant and sanction the Assembly. Accordingly, though not a member of it, he took his place in the Assembly as their chief director; and thus encouraged, they proceeded to abolish episcopacy for ever, to deprive all the bishops, and to excommunicate the greater part of them and all their abettors. Charles, and James before him, had completely conferred all the power of Parliament on the bishops, making eight of them the Lords of the Articles, with authority to choose eight of the nobles, and these sixteen having power to choose all the rest, so that all depended on the bishops, and they, again, on the king. This effectually ranged the nobles against them. The Marquis of Hamilton, notwithstanding his fears, was permitted quietly to withdraw to England, whence he was soon to return against them at the head of the fleet. The people received the news of the proceedings of the Assembly with transports of joy, and celebrated the downfall of episcopacy by a day of thanksgiving. Charles, on the other hand, issued a proclamation declaring all its acts void, and hastened his preparations for marching into Scotland.

But the Covenanters were not the less active on their part, and everything tended to a civil war, the result of Charles's incessant attacks on the liberties of the nation. They made collections of arms, and as early as December they received six thousand muskets from Holland. These had been stopped by the Government of that country, but Cardinal Richelieu had suddenly shown himself a friend, by ordering the muskets as if for his own use, receiving them into a French port, and thence forwarding them to Scotland. However impolitic it might appear for France to assist subjects against their prince, it must be remembered that Charles had managed to create nearly as strong a feeling against him in Louis and his minister Richelieu as in his own subjects. He had set the example by assisting the Huguenots against their prince, and had provoked France by defeating its plan of dividing the Spanish Netherlands between that country and Holland. The present opportunity, therefore, was eagerly seized to make Charles feel the error he had committed. Richelieu, moreover, ordered the French Ambassador in London to pay over to General Leslie, one of Gustavus Adolphus's old officers, who had been engaged by the Assembly, one hundred thousand crowns. This last transaction, however, was kept a profound secret, for the Scots, when advised to seek the assistance of France and Germany, had indignantly refused, saying the Lutherans of Germany were heretics, and the people of France Papistical idolaters; that it became them to seek support from God alone, and not from the broken reed of Egypt. The preachers thundered from the pulpits against the bishops, and the determination of the king still to force them on the country; and they refused the Communion to all who had not signed the Covenant. The Tables called on the young men in every quarter of the country to come forward and be trained to arms, and the Scottish officers who had been engaged in the wars in Germany flocked over and offered their services for the support of the popular cause. The nobles contributed plate to be melted down, the merchants in the towns sent in money, and an army of determined men was fast forming.