While the land question threatened to divide the Old-Irish of Ulster from their co-religionists of the South, the Assembly deliberately—perhaps because it could not help itself—adopted a scheme of military commands which from the outset made for disunion. Owen Roe O’Neill was chosen General for Ulster; Preston for Leinster; Garret Barry for Munster, and Colonel John Burke for Connaught, the last with the title of Lieutenant-General, as it was hoped the Earl of Clanricarde would take the chief command in that province. No Commander-in-Chief was appointed, and nothing like concerted action between the various armies was ever seriously attempted. O’Neill had, moreover, little friendship for the Supreme Council, and was on bad terms with the Leinster General, Preston, who was father-in-law of Phelim O’Neill, Owen’s rival, who had but lately claimed the chieftainship of the O’Neills on the ground of lawful heirship, while Owen Roe, though possessing incomparably greater personal merit, was sprung from an illegitimate branch. Of the continued state of war which existed, it is impossible to give any detailed account here. It was a series of skirmishes and petty sieges, in which one side harassed the other without either gaining a decisive victory. The Royalists, under Ormond in Leinster, and the other English General, Murrough O’Brien, Lord Inchiquin in Munster, were in the greatest distress for want of provisions, pay, and munitions, and concerted action by the Irish forces under a skilled commander like Owen Roe, for instance, would soon have forced them to terms, but no such united effort was made. The Scottish army, which had landed in Ulster under Leven and Monroe, remained under the command of the latter, and possessed itself of the greater part of the province and extended its raids and forages as far as Sligo, but for the most part afterwards remained inactive, and was only distinguished by some massacres of the unarmed peasants. Of the general conduct of the war, Gardiner says: “There was no strategy on either side, it was an affair of skirmishes and sieges, of raids over the wide expanse of pasture-land, for the purpose of sweeping off the herds of cattle which were the main wealth of the people. Wherever an English force could penetrate, its track was marked by fire and the gallows. Exasperated at the Ulster murders, and seeing in every Irishman a murderer or a supporter of murderers, the English soldiery rarely gave quarter, and, unless the accounts of their enemies are entirely devoid of truth, when they did give it, it was often violated. The peasants retaliated by knocking stray soldiers on the head, and by slaughtering parties too weak to resist. Yet, whenever ... the Irish forces were commanded by officers of rank and authority, they were distinguished for humanity under circumstances of no slight provocation. The garrisons of fortified posts captured by the Irish, were uniformly allowed to find their way in safety to a place of refuge. On the whole, the balance of advantage was on the Irish side.”

The history from now until the arrival of Rinuccini is almost entirely that of a long series of tedious negotiations between Ormond, acting for the King, and the Supreme Council, for a cessation of arms. Ormond had recently been made a Marquis, and his commission as Commander-in-Chief of the English troops had been enlarged, so as to leave him independent of the nominal Lord Lieutenant, the Earl of Leicester. Parsons still remained Lord Justice, and the King, did not venture to interfere with him. Leicester had got as far as Chester on his way to Ireland, but Charles, foreseeing that he would side with Parsons and make him still more powerful, summoned him to Oxford, this being practically the recall of his commission as Lord Lieutenant. The English interest in Ireland therefore remained in the hands of the Lords Justices, nominally acknowledging the King, but in reality, devoted to the Parliament and the policy of confiscation, and in those of the Marquis of Ormond, entirely devoted to the King, but with some sympathy for the Catholic nobility and gentry, especially those of the Pale, as he saw they had been driven through despair at the threatened confiscation, to join the Old-Irish in their uprising.

Reynolds and Goodwin had been sent over by the Parliament with £20,000, to attempt to win over the English garrison. The King, when he heard of their presence at the sittings of the Privy Council, denounced them as rebels, and severely reprimanded the Lords Justices. Soon after, he sent warrants for the arrest of Reynolds and Goodwin, but they had fled to England.

Charles, by this time at his wits’ end for forces to check the growing strength of the insurrection in England, had turned his thoughts to Ireland, and determined to enter into negotiations with the Confederates for a cessation so as to enable him to withdraw the English garrison from Ireland. He had proposed to make Ormond Lord Lieutenant, but left it to him to accept or decline the office. Ormond, however, advised him “to delay the sending him an authority to take that charge upon him,” and proceeded to the treaty with the Confederates as Commander-in-Chief of the Forces. Amongst the reasons other than the King’s wish, which influenced Ormond in seeking a cessation, were the almost complete exhaustion of supplies of money and food for his troops. The £20,000 brought by Reynolds and Goodwin were spent, having for only a short time barely sufficed, as Carte pithily puts it, “to give soldiers twelve pence a week to keep them from drinking water.” Though Ormond had defeated Preston at Ross, he had no provisions to enable him to keep the field, and was at once obliged to return to Dublin with a starving army clamouring for food and pay. The Lords Justices besought the English Parliament to send money, but the Parliament wanted all the money they could lay hands on, including that subscribed by the Adventurers for the Irish War for their own war against the King, so that it may be truly said that the liberties of the English people were literally paid for by the spoliation of the Old-Irish and Anglo-Irish proprietors.

In January, 1643, Charles issued a commission to Ormond, Clanricarde, and others, to treat with the Catholic leaders, and this step was, of course, at once resented by the Lords Justices. The officers of the English garrison made some protest, but weary of waiting for supplies, which the English Parliament was unable to send, Ormond succeeded in getting them to place their hopes in the King’s power to satisfy their complaints. The King’s Commissioners and those of the Confederation met at Trim on St. Patrick’s Day, 1643, and the latter presented their Remonstrance of Grievances. In that document they described the disabilities they were under on account of their faith, the exclusion of their sons from University education and public employment, the tricks and chicaneries of the Puritan officials striving to make fortunes out of their unhappy position, Parsons being the worst of these; the boast of Parsons and others, that Catholics would be forced to change their faith, and the intention of the English Parliament to pass Acts for the extirpation of the Catholic religion in the Three Kingdoms. It denounced the misconduct of the Lords Justices, their dependence on the English Parliament, the Confiscation Acts passed at their instigation, which had forced the Anglo-Irish to take up arms in self-defence. It declared the Irish Parliament completely independent of that of England, and that the latter had no right to legislate for Ireland. That the Irish Parliament had sunk under the Lords Justices to be a mere section of their own partisans, where the majority of the members of the House dare not appear. The document concluded by praying for a Free Parliament, in which all matters affecting Ireland might be discussed irrespective of Poynings’ Act, and that no Catholic should be, on any account, excluded from sitting and voting. If these favours were granted to them, the Confederates were ready to send an army of 10,000 men to England to defend the King’s prerogative.

Against this remonstrance, the Lords Justices sent a strongly-worded protest to the King against his entering into any treaty with the Irish. They recalled the events of the first rebellion; the Irish did not really care for their religion, but were so ungrateful for the care the English had taken of them as to massacre 150,000 men, women and children of that nation.

“Astounding as this statement was,” says Gardiner, “there was one point in the argument of the Lords Justices which had been passed over entirely by the Irish Commissioners. If the Irish, after all that had passed, were suffered to consolidate their power, would they allow the English to live on an equality with themselves?... Cynicism, however, has seldom gone further than the cool anticipation of slaughter which followed. They remember, say the writers, ‘that in the best of former times the Irish did so exceed in number, as that the Governors never cared or durst fully execute the laws for true reformation for fear of disturbance, having some hope always by civil and fair entreaty to win them to a civil and peaceable life; so if peace should now be granted them before the sword or famine have so abated them in number as that in a reasonable time, English colonies might overtop them.’ ‘No peace,’ the Lords Justices repeated, ‘could be safe or lasting till the sword have abated these rebels in number and power.’”

Ormond, while considering the proposals of the Confederates as totally inadmissible, condemned the representations of the Lords Justices as tending to countenance a scheme of extirpation iniquitous in the attempt, and impossible to be executed.

Charles was desirous of coming to terms with the Catholics without giving them any real power, so that he might strengthen his army in England. Though the manner in which even the rumour of an Irish Catholic army was received in England showed how dangerous it was for Charles even to think of it, still, by entering into negotiations he might gain time in Ireland, and be enabled to withdraw the English garrison—at any rate, temporarily. He first dismissed Parsons, and appointed Sir Henry Tichborne Lord Justice in his place, while Borlase, too old and inefficient to be of consequence, was allowed to remain. The King next authorized Ormond to treat for a cessation of arms for a year, and privately wrote to him to bring over the Irish garrison to Chester as soon as the cessation was agreed on.

The cessation was not, however, so speedily arranged as the King desired, and the Confederates were not so anxious to see Charles enter London in triumph as to forego the interests of religion and country. The earlier negotiations were broken off on Ormond’s refusal of the free Parliament asked for in the Remonstrance of Grievances. Nevertheless, delay was favourable to the Confederates, and their power was still extending over the country. In June, 1643, Ormond, conscious of his desperate military position, “and,” as Gardiner thinks, “perhaps willing to establish beyond dispute, the necessity of coming to terms with the insurgents, told the Lords Justices that he was ready to break off the negotiations if they could find any possible way of maintaining the troops.” They were unable to help him in any way, and Ormond set out once more, this time with the reluctant consent of the Castle Government, to attempt to come to terms with the Confederates, but after nearly three weeks of fruitless effort, he resolved to attack Preston once more. Preston wisely avoided a battle, and Ormond’s army in a starving condition, was obliged to retreat to Dublin.