The earliest engagement in which MacColla is involved is still unknown, he is closely associated with the O'Cahans namely Donal Chief of the O'Cahans and he subsequently befriended Manus Rua O'Cahan an officer of an O'Neill regiment on the continent. The Rising of 1641 was primarily an O'Neill enterprise, the O'Neills where traditional enemies of the MacDonnells in Ulster, in fact they where historically closely allied with the Campbells. It was really only in the time of Hugh O'Neills Nine Years war that ALL the Ulster clans united in one last do or die rebellion. However the Marquis of Antrim's mother was an O'Neill, and his Daughter had married one, this would make them all kinsmen in the Gaelic sense. However as the enterprise was not a MacDonald one this would rule out any initial involvement by MacColla or his clan. There is no doubt however that when the storm of 1641 broke in Ulster in November of that year, MacColla and his disaffected clan joined in the melee after the initial engagements.

In the spring of '42 he and his levies joined up with the Confederate forces in Ulster under Sir Phelim O'Neill[not Owen Rua O'Neill]. Where he commanded a regiment.

•MacColla was involved in the Sack of Dundalk, Newry, and Armagh at the end of December of 1641/January 1642. •He was possibly involved in the great pillaging of the Pale[The greater Dublin area as far as the Boyne], however more likely was the general wasting of NE Ulster and its environ's in the Winter of 41/42 causing the alleged deaths of up to 45,000 English Protestants in Ulster. •The siege of Drogheda 1641/42 and the Battle of Julianstown. A the battle of Julianstown County Meath in 1642 where elements of the Ulster Rebels under the leadership of Sir Rory O'More Baron of Ossory, in which MacColla's regiment was a part off, ambushed and slaughtered the English Relief forces for Droheda under Col. Roper at Julianstown Bridge 3 miles from the town. Only Colonel Roper with 50 men made it to the town. •In February 1642 the siege of Droheda was raised after two attempts at a storm where repulsed. The Governor of the town Sir Henry Tichborne relentlessly pursued the retreating Ulster Rebel army, Newry and Dundalk where both sacked, the inhabitants put to the sword. •1642 April the Battle of Ardee in which elements of the retreating Ulster army of Sir Phelim O'Neill where resoundly beaten by Sir Henry Tichborne. Trim falls to Sir Charles Coote Senior, but to the joy's of Catholics this psycho was mortally wounded. •May 1642 MacColla was victorious at Ballymoney (Blaney), first recorded use of the "Highland Charge"?????????????? In which the forces of Sir Robert Stewart where routed. •June 1642 he was defeated at Glenmaquin near Raphoe with the forces of Sir Phelim O'Neill, MacColla was wounded. •June 1642 the forces of Sir Phelim O'Neill where defeated on the river Blackwater, in full retreat the City of Armagh was fired and sacked by MacColla's regiment.

Note: at this time the conflict was extensive throughout Ireland, this chronology is confined to the Ulster theatre as it is the one in which MacColla is closely associated. The barbarity of this conflict is staggering by even 17th Century standards, no one was spared, generally the Govt. be they Royalist or Parliamentarian launched forays from the towns and strongpoints they held. On a foray anyone they met was ruthlessly butchered. When Sir Charles Coote was reprimanded by one of his English Cavalry Officers in regard to the impaling of infants on Pikes, he replied "Nits become Lice". So it is important to bear in mind this is the type of conflict in which the Irish levies destined for Scotland where brutalised by.

•In June 1642 all over Ireland the Irish where on the retreat and just as their cause appeared to be lost, three events happened. The Spanish Major-General Owen Rua O'Neill arrived in Donegal with three hundred officers and arms for 5,000 from the Spanish army of the Netherlands, chief among his officers was his best friend[Owen Rua did not have ANY other friends] Manus Rua O'Cahan. The Spanish Colonel Preston arrived from Flanders with a large fleet, a thousand fighting men, arms for 12,000, cannon, and money. The Catholic Clergy called a convention in Kilkenny which united and pooled all the resources of the Old English, Gaelic Irish, Towns, and the church. This is called the Catholic Confederation of Kilkenny[Protestants where not excluded, one of the Confederates ablest commandeers Lord Castlehaven was a Protestant]. Security of tenure, loyalty to the Stuarts, freedom of religion, repeal of the anti-Gaelic laws, these where the modest aims. •In July Owen Rua O'Neill described Ulster as "Hell on earth if there be such a place", he carefully avoided the larger and better trained forces surrounding him, particularly the Scottish Covenanter army under Leslie and Monroe. Owen Rua retreated into the remotest parts of the Irish midlands, in this area of dense woodland, lakes, marshes and bog, he trained his armies, and sallied out on foray's against Leslie's and Monroes Scots in particular, whenever the opportunity presented itself he relentless wore them out by carefully avoiding a pitched battle but by endless and relentless guerrilla tactics. However By 1643 he was ready and the campaigning of 1643 brought some notable successes in which MacColla and Manus Rua befriended each other. Leslie left Ulster and gave a note of warning to Monroe "If MacArt[Owen Rua] gathers an army he will defeat you". •In March 1643 Owen Rua and MacColla where victorious at Bendannagh and a great follow up victory at Kilrea, in which some elements of the Confederate forces of Owen Rua O'Neill under Alaister MacColla's regiment defeated the Ulster Royalists army under General Stewart this was all but wiped out, but in which thousands of Protestant refugees where slain on the road to Belfast [not much is written on this]. •At Angalwey 1643 and at Charlemont Fort, O'Neill twice routed the Covenanter Army under General Monroe, in one engagement O'Neill with only 250 cavalry faced Monroe with 5,000 and scattered his army. Monroe was incensed and re-grouped and was resoundly beaten outside the Charlemont fortress, MacColla almost single handily charging the enemy, who fled in terror. •At Clones in March of 1643, on a hunting expedition, O'Neill was caught by Monroes dragoons in the open, narrowly escaping with his life, only for the prompt thinking of Manus Rua O'Cahan, O'Neill would have been killed. •In June 1643 Owen Rua O'Neill was victorious at the River Boyne ford of Portlester Mill, after soaking up heavy cavalry charges from Generals Moore and Montgomery, MacColla at a critical juncture launched his highlanders using his famed "Highland Charge". This charge coupled with the extraordinary death of the Round Head Parliamentary Commandeers in Ireland, Gen. Moore[he was personally decapitated by a cannon ball fired by O'Neill himself looking through a perspective glass and demonstrating to his officers how to fire a cannon properly], this led to the complete destruction of the Parliamentary forces in Ireland. It took nearly three years for the Parliamentary Forces to recover. Particularly as the Civil War in England began to take its toil. •The King was desperate for a truce in Ireland, he needed reinforcements badly. His great scheme was to get the Duke of Ormond to sign a truce with the Confederates, offer them peace, and indeed if necessary come to Ireland, Unite everyone and at the head of a great army return to England. That was the plan however this hopelessly split the Confederates and set O'Neill against the Old English, O'Neill's authority was the See of Rome not the King of England, the Old English where Royalist's first, coupled with their traditional enmity for each other this was the defining moment for the Confederation, more so than any battle fought on the field, they where in fact doomed by their disunity.

A lull and a general truce in the fighting in 1644 allowed O'Neill, The Earl of Antrim, and MacColla to recruit levies from the MacDonalds and from among O'Neills army to take to Scotland. An O'Neill regiment under Manus Rua O'Cahan, A MacDonald regiment under MacColla, and another regiment made up of Leinster Palesmen[Old English]. They left the Fort of Duncannon in Waterford in late 1644 under the command of MacColla.