The Kilkenny Confederacy sent 2,000 troops in three regiments under the command of Alasdair MacColla to support Montrose's Royalist army in Scotland who were fighting against the Covenanters in 1644. During the years 1643 and 1644 they also promised to send 10,000 troops England and Wales. However they ultimately never sent the troops because their negotiations with Charles I broke down over the public practice of Catholicism and the independence of the Irish Parliament.. However, a ceasefire deal between the Irish Confederates and English Royalists did result in the return of some 5,000 Royalist troops from Ireland in 1643-44. The confusion of these regiments with the Irish Catholics, associated in Parliamentarian minds with the massacres of the Irish Rebellion of 1641, did much to frighten English Protestant opinion. English Parliamentarians had often taunted Prince Rupert that he was a German mercenary, and while they could just about tolerate foreign Protestants and English Roman Catholics fighting as Royalists, they considered support by foreign Roman Catholics a much greater threat.
The relative absence of Irish Catholic soldiers in England meant that the Ordinance was rarely acted upon. One exception was the massacre of some Welsh civilian camp followers (who were mistaken for Irish) by Parliamentarian soldiers after the battle of Naseby in 1645. The Welsh, mostly women, were speaking the Welsh language, which the Roundhead troops mistook for Irish. Historian Charles Carlton has commented that the incident, 'was so unusual that it caused considerable comment'
Irish military historian Pádraig Lenihan explains that in practice although the war at sea was covered by the Ordinance, as the Irish privateers captured more English sailors than the English did Irish and held English prisoners to exchange them for Irish prisoners, the ordinance for naval warfare lapsed. As he explains "The 'laws' of war evolved like any primitive legal code, from the principle of reciprocity; self-interest counselled against brutality if there was the chance of being paid back in the same coin".
In Ireland, the Irish Confederate Wars were waged with considerable brutality. Irish military historian Pádraig Lenihan makes the point that the Ordinance "... illustrates the depth of the conviction that the Irish shared a common and irredeemable blood guilt. The pitiless execution of Covenanters by Mac Colla's followers would seem to show that for the Irish, too, battle against British forces was waged without moral restraint. In practice, however, [In Ireland] there were restraints. For example, O'Neill, immediately after Benburb, sent 150 prisoners (excluding officers, whom he kept for ransom) under escort back to Scottish quarters (Hogan, war in Ireland)."
In England as in Ireland and on the high seas, expedient reciprocity often won over other principles. For example at the start of the First English Civil War Major John Lilburne was captured at the Battle of Brentford. Not only was he the most senior Parliamentary officer captured during the first campaigning season, he was also well known for his radical views. Plans to try him for "bearing arms against the king" were dropped when the Parliamentary side threatened to retaliate in kind, and he was exchanged for a Royalist officer. At the end of the Second English Civil War and the apparent utter defeat of the Royalist cause, the Parliamentary side was far less lenient than at the end of the first war. In the view of the Parliamentarians, Royalist leaders who had participated in the second war (and who in some cases had broken their parole given at the end of the first war not to take up arms against Parliament) had caused pointless bloodshed for a lost cause, and so, for example, three of the five prominent Royalist peers who fought in the second war and were captured by the Parliamentarians were beheaded at Westminster on 9 March 1648. This opinion reached all the way to the top or the Royalist cause, with the Grandees of the New Model Army, who before the second war had wanted a negotiated settlement with Charles I, reluctantly coming round to the radicals point of view that "Charles Stuart, That Man of Blood should be tried and executed — as he was in January 1649.