In February, the Scottish Army in England withdrew into Scotland and Charles I fell into the hands of the Parliamentarians. Parliament also informed the Army of Ulster that its services were no longer needed in Ireland, but with no agreement on pay, it remained in place. The Scottish Parliament protested the abduction of King Charles and Scotland and the King began secretly negotiating Scottish military intervention on his behalf in England. On 7 June 1647 Colonel Michael Jones and regiments of the New Model Army arrive in Ireland. On the 19 th of June Ormond turned Dublin over to Parliament and departed Ireland for France and exile. In June Preston and his Leinster army, took Fort Carlow, with Fort Naas and Fort Maynooth falling to him in June. Preston then besieged Trim but the siege was lifted by Jones. On the 17 July 1647, Monck took command of Parliamentary and settler forces in Ireland while Coote commanded the Lagan Army for Parliament. A combined force of Parliamentarians under Jones and forces under Sir Henry Tichbourne, the governor of Drogheda, defeated Preston at Dugan’s Hill 8 August 1647.
The Earl Inchiquin seized Cashel on Sep 1647 leaving no prisoners and defeated Taffe and Alasdair McColla’s forces at Knockanauss on 13 Nov 1647. By November King Charles had fled to the Isle of Wight and in December, he and Scottish commissioners had agreed to an “Engagement” exchanging a Scottish invasion of England for the union of the two nations and three years of Presbyterianism in England. The Engagement split the government of Scotland between those who supported the Engagement and those who did not.
On 3 April 1648 Lord Inchiquin renounced Parliament after the arrest of King Charles I, declared for King Charles I and began negations for a truce with the Confederation. The Supreme Council agreed to negotiate and declared Rinuccini, O’Neil and their followers all traitors. Rinuccini opposed the peace but was not supported by the majority of the Supreme Council whom he excommunicated for opposing him. O’Neil supported Rinuccini by declaring war on the Supreme Council. The Supreme Council was supported by Clanricarde, Preston and Taffe in its efforts to make peace with the royalists. O’Neil’s Ulster army marched on Kilkenny, the Confederation capital, but was eventually driven back by the combined forces of Inchiquin and Preston.
In May the Scottish Parliament voted in favor of war with Parliamentarian England and began recruiting soldiers for an army to invade England. Robert Monro sent elements of his forces under the command of his nephew George Monro to reinforce the Duke of Hamilton and “the Engagers”, as they were known. The Engager army having invaded England, was destroyed at Preston in August. George Monro and his forces, left in reserve in Scotland, departed Edinburgh in the face of the anti-Engager “Wiggamore Raid” of lowland Scots on 31 August. George Monro returned to Ireland after Engager regime was eliminated in September.
In September 1648 the remnants of the Army of Ulster refused to surrender Carrickfergus, Coleraine and Belfast to Jones and his Parliamentarian forces and return to Scotland. Carrickfergus was taken by treachery with Sir George Monro thrown in the Tower by Monck until his release and retirement in Ireland in 1654. The Scottish Army of Ulster was disbanded shortly thereafter. At least one of the regiments went into English service and some of the officers and soldiers of the disbanded regiments did as well.