The rebellion of 1641
The Scots in Ulster were no better off than the Irish landowners by 1630 having highly mortgaged their lands due to their inability to transition to a market economy. This resulted in an uprising against the government. October 22 1641 the rebellion took hold causing disorder throughout the country. The rebels, under Sir Phelim O’Neill, an Irishman himself, took over most of Ulster. Originally, the Scottish settlers were to be spared but the rebels soon fell out of control and massacres of settlers took place. Thousands died, some from battle, others from exposure and disease. Those who were able, fled to Dublin or back to Scotland and England.
It was not until the arrival of Oliver Cromwell in 1649 that the country was brought under control. The Scots supported Prince Charles I, son of King James. He reigned from the time of his father's death in 1625 until he was executed in 1649, tried for high treason. Over the next few years, the monarchy was abolished and a republic formed called the Commonwealth of England. The monarchy was restored in 1660 to Charles’ son Charles II.
It would not be until the monarchy was restored to Charles II that the Ulster Scots would breathe a sigh of relief. During the years between 1649 and the re-instatement of the monarchy, they were subjected to heavy fines if they did not want their land confiscated.
By the second half of the 17th century the Presbyterians emerged in Ulster as a distinct denomination between it and the Church of Ireland. Most of the Scots were of the former persuasion