In Ireland the persecution of the Presbyterians had sown the seeds of rebellion by the native Irish under Sir Phelim O'Neill who sought to rid themselves of British rule and recover forfeited lands. The initial outbreak on October 23, 1641, was to seize Dublin Castle but this failed.

Elsewhere, however, the insurgents ransacked towns and massacred its inhabitants with Protestants of any faith a primary target. This was the "Killing Time" in Ireland.

Some of the major towns such as Enniskillen, Londonderry, Coleraine, Carrickfergus, Lisburn and Belfast received timely warning and were able to prepare for and repulse attack . But other small towns and the countryside in general were ravaged. Protestant homes, farms, churches, minister`s houses were torched and the occupants stripped naked and left cowering in the hedgerows in what was one of the severest winters in memory. It was said that the river Blackwater in County Tyrone turned red with the blood of the murdered populace.

Some historians allege that the 1641 Rebellion was not as bad as some might paint it. However, there are 32 volumes of sworn depositions in the library of Trinity College, Dublin that give a horrific description of events. These tell of children having their brains dashed out against a brick wall; or being thrown into pots of boiling water. Of people having their eyes gouged out, hands and ears cut off; of being buried alive; of women stripped naked and cut up with knives; and even strips of flesh cut from a victims who were roasted alive.

At Loughgall some 300 men women and children were stripped of their clothing and locked in the church. They were then selectively assaulted and brutalised, raped, butchered, broiled over hot gridirons and hung drawn and quartered. At Portadown is is reported that 196 persons were hurled into the river and drowned in one day; and that about 1000 in all suffered in this way.

Ministers of the Church were dealt with extreme cruelty, hung, dismembered, and one, Thomas Murray of Killyleagh was actually crucified with the bodies of two English gentlemen suspended either side of him in mockery of the Crucifixion.

In the fields and hedgerows multitudes suffered privation, cold and disease. Bodies lay where they were and the smell of death pervaded everything. A plague broke out and it is said that 6000 died in Coleraine while Belfast, Carrickfergus and Lisburn also suffered badly.

Into the fray came Major General Munro and 10,000 Scottish troops who arrived in Carrickfergus in February, 1642. Importantly the soldiers were accompanied by their own chaplains who were to play a prominent part in the Presbyterian rebirth in Ireland. These chaplains organised a Session in each regiment and when there were four they created the first regular Presbytery on June 10, 1642. The ministers were Hugh Cunningham who settled at Ray, County Donegal; Thomas Peebles at Dundonald and Holywood; John Baird at Dervock, and; John Aird and John Scott who later returned to Scotland.

Support from Scotland soon helped the re-establishment of Presbyterian congregations but more tribulations were to follow.

An interesting event involving the Covenanters occurred in May, 1644. The English Parliament appointed General Munro Commander-in-Chief of all the English and Scottish forces in Ireland on April 27, 1644. Sir James Montgomery, knowing of this, called his officers together on May 12 with a view to arranging the hand-over of command to Munro who was, at the time, in Carrickfergus. Scouts sent out were captured and, under orders from Munro, deliberately misreported no sign of movement towards Belfast and the guard was relaxed. But Munro had speedily marched through the night and caught Belfast by suprise, much to the amazement of the British Colonels.

Munro's excuse was that he did not feel safe in the town without his own troops, and besides there those, meaning Col. Chichester and his regiment, who had declined to accept the Solemn League and Covenant.

In the course of this seizure of Belfast a troop of soldiers of Col. Arthur Chichester's regiment had been stood down at Stranmillis, on the outskirts of Belfast. Munro had ordered that they march with drums beating and colours flying to the Market Place and there they were required to ceremonially shred their colours as an indication of obedience to the Scottish army and the Covenant. The duplicity seems to have been unnecessary as the British Colonels placed themselves under his command forthwith but is indicative of the mistrust that existed between the so called allies.

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