So in this timeline, is Scotland mostly catholic?
Edit: Also, some of the major players in 1640s Ireland
James Butler, Earl (later Marquess and Duke) of Ormonde
Loyalty: Royalist English
Ethnicity/Religion: Old English/Protestant
Bio: The leader of Royal English forces in Ireland, Butler is extremely loyal to the crown and a competent general. As the representative of the crown in Ireland, he had the already difficult task of trying to reconcile the interests of the Crown, the Gaelic aristocracy, his fellow Old English aristocrats (who unlike him are mostly catholics), and the new plantations of protestant English and scots.
Historically, when faced with the reality that he could no longer hold Dublin, he surrendered it to the Parlimentarians as the lesser evil, which he came to regret when said rebels eventually executed the King he served so faithfully. His loyalty and service to Charles' I & II would be rewarded greatly during the restoration.
Owen Roe O'Neill
Loyalty: Spain, Ulster
Ethnicity/Religion: Gaelic/Catholic
Bio:A nephew of Hugh O'Neill ("the Great O'Neill to the Irish) he followed him into exile and has spent his career serving in the Spanish army's Irish regiments. He'd served with distinction in the Eighty Years War, including a few heroic defenses of cities besieged by Dutch or French forces. He'd been active in several schemes aimed at encouraging Spain to invade Ireland.
Historically, in 1640 he was still in the Spanish service, with the O'Neill's in Ireland led by his kinsman Sir Felim O'Neill, who was largely pushed to the sidelines when Owen Roe landed with a band of veterans in 1642. Owen Roe was a larger than life figure who lead the northern irish armies through most of the war, but also an extremist who did not work well with others, especially some of his former comrades in Spain's Irish Brigades.
Felim O'Neill
Loyalty: Ulster
Ethnicity/Religion: Gaelic/Catholic
Bio: The leading O'Neill at the start of the rebellion, Felim was very different from Owen Roe. He was trained as a lawyer in England and tried to protect his people's lands from encroaching plantations legally. When civil war broke out, Sir Felim led a plot to seize Ulster from the Protestant settlers. It was successful as far as it went, but he swiftly lost control of the mobilized peasantry which set off a sectarian massacre that remains controversial in the 21st century. This has tainted his historical legacy and overshadowed his role as a comparatively moderate voice in the politics of Ulster and the Confederacy.
Thomas Preston
Loyalty: Leinster
Ethnic/Religion: Old English/Catholic
Bio: Like Owen Roe, Thomas Preston served in Spain's Irish Brigades in the 80 years war with distinction. The two Irish leaders managed to form an intense personal hatred for each other during those days, for reasons lost to history. As it happens, Thomas Preston is also the father-in-law of Sir Felim O'Neill, whose second wife is Preston's daughter. Like Owen Roe, he returned to his native soil after the rebellion was well under way. He would be placed in command of the armies in Leinster, where he received the most funding of the Irish armies, a source of constant irritation to the other generals. His record is decidedly mixed, losing major field battles but also leading some impressive siege defenses.
Garret Barry
Loyalty: Munster
Ethnic/Religion: Old English/Catholic
Bio: Much less famous than his fellow rebel leaders, Berry was also a professional soldier in the Spanish service during the 80 years war. He authored several books on how to train and discipline an army. This academic knowledge did not translate into actual performance in the field. His Irish levies would be routed by a smaller, better equipped force at the Battle of Liscarroll, after which Garret Barry was discredited as a leader and took no major role in the wars. By dumb luck, he happened to be in Ireland recruiting soldiers for Spain's Irish Brigades when the rebellion broke out.
Murrough O'Brien, Baron (later Earl) of Inichquin
Loyalty: Self
Ethnic/Religion: Gaelic/Protestant
Bio: A remarkable historical oddity, he is known to this day as Murchadh na dTóiteán ("of the conflagrations"), a nickname he has not yet earned in 1640. He is said to have studied war (but not actually fought for) with Spanish forces in Italy. As The O'Brien he's a direct descendant of Brian Boru and other O'Briens who ruled Thomond with de facto independence even after their nominal submission. He was fostered by, and married the daughter of,
William St Leger, President of the English plantation in Munster, a man infamous for cruelty and harsh rule, who would die in 1642 having failed to suppress the revolt.
O'Brien supported the plantation process, even becoming vice-president of the Munster plantation, which in turn helped protect his lands from confiscation. Historically he first sided with the Royalists, leading their armies successfully against Garret Barry. With little material support from the King's government, he supported his troops mainly through pillaging and confiscations, earning him his nickname. Later, having been denied material support and feeling snubbed personally, he switched his allegiance to Parliament, and pillaged in their name. When Parlimentary troops actually began to campaign in Ireland, O'Brien and his army conquered the south of Ireland for himself, eventually returning to nominal allegiance to the Crown and an alliance with many of the more moderate catholic rebels. During the Cromwellian invasion, he attempted to get the remnants of Irish resitance to rally to him as the last line of defense, but being a protestant and having burned so many bridges (literal and metaphorical) he fled into exile.
He became involved in various plots, finding service in France. There he found his beliefs to be inconvenient to his ambition to lead France's Irish soldiers and lead a French backed future war in Ireland, so he converted to Catholicism, which helped him little there but would cause him enormous problems after the Restoration. Still he managed to weasel his way into Charles II's good graces, regaining his lands and titles and even commanding a small expeditionary force to support Portugal against Spain.