Cromwell sent an army under General George Monk with the overt design to secure Ireland under Parliamentary control. The underlying mission of the Parliamentary army was to wreak vengeance on the Irish Catholics who had started the rebellion, and who, it was believed, had murdered all the Protestants in Ireland. When Monk failed to subdue the Royalist sympathizers, including the Scots in Ulster, Cromwell himself led a force to the island in 1650. Cromwell's expedition to Ireland had three purposes. First and foremost was the subjugation of the Catholics and Presbyterians who had rallied behind the Royalist banner. The second purpose was to remove anyone associated with the Irish rebellion. The third objective was to convert all of Ireland to the Puritan faith. The rebellion was not put down due to the outbreak of civil war in England and Scotland - the Wars of the Three Kingdoms until the 1650 Irish Confederate Wars.
An estimate has been given that approximately 616,000 people died during the course of the campaign, some from famine and plague incidental to the actual warfare. The majority of those deaths, though, were native Irish. In addition to the casualties of war, Cromwell had many of the survivors, primarily native Irish, but also some English and Scot Royalists, deported to the West Indies. He made many allowances to the Presbyterian Scots in Ulster which enabled them to flourish as part of the Protectorate Commonwealth.
A large number of the residents of the Ulster settlement were slated to be deported, but Cromwell relented and allowed them to stay in Ireland. Many of their estates were confiscated and they were forced to move to the province of Connacht to the west of the Shannon River. Through sheer force, Oliver Cromwell brought an end to the Irish rebellion begun in 1641, and the Scots in Ulster experienced peace for the first time in a decade.
Those who stayed in Ireland afterward in the north west of Ulster, the Planters around Derry and east Donegal organised the Lagan Army in self defence. The descendants of the Presbyterian planters played a major part in the 1798 rebellion against British rule. Scotland had its own parliament in the 17th century, and was substantially independent, even setting its own colony up in Darien. Another wave of Scottish immigration to Ireland took pace in the 1690s, when tens of thousands of Scots fled a famine in the borders region of Scotland to come to Ulster. It was at this point that Scottish Presbyterians became the majority community in the province. These planters are often referred to as Ulster-Scots.
When, in 1660, the Stuart monarchy was restored, there was the possibility of Catholic persecution, but Charles II proved to be as lenient as Cromwell towards the Presbyterian Scots. Ulster prospered throughout the latter part of the Seventeenth Century. Woolen manufacture had increased during the Protectorate period and there was a migration of English from the northern counties of England to North Ireland. A large number of Scots from the Lowlands fled to Ulster. Advocates of the Solemn League and Covenant had not been silenced by the Puritan Cromwellian Protectorate and became known as the Covenanters. King Charles II advocated the Covenant only in order to obtain the Covenanters' aid in his restoration to the throne of England. As soon as he was re-established as king in 1660, Charles II began to institute a series of restrictive measures that were aimed as stripping the Presbyterian ministers of their rights and privileges. The 1680s in Scotland saw increased conflict between the Covenanters and the governmental forces and many Scots migrated to Ulster where there was relative peace and quiet. The peace which Ulster experienced from Cromwell's Protectorate government through the early 1680s ended when King James II came to the throne.
Not all of the planters were Lowlanders. A migration of Huguenots to Ireland in 1685 when the French government revoked the Edict of Nantes which had protected religious liberties since 1598. The Huguenots were Protestants whose religious beliefs were similar to those of the Presbyterians in Scotland and Ulster. Irish nationalists, most of whom are Catholic, identify with the native Irish who were displaced in the Plantation; Unionists, most of whom are Protestant, identify with the planters. Intermarriage has occurred across the sectarian divide: many Roman Catholics in North Ireland are actually descended from the Planters, and many Protestants from native Irish families, as evidenced by their surnames - although of course the surname only denotes one paternal ancestor. There is a permanent exhibition dedicated to the Flight of the Earls and the subsequent Plantation in Draperstown in North Ireland and at the "Flight of the Earls Centre" in the Martello Tower at Rathmullan.
The Great Migration from Ulster to America began in 1717. In some instances Ulster families had immigrated to the New World before 1717, but those instances were few and isolated. Not all of them succeeded. In 1636 a group left Ireland but had to return because of violent storms enroute. A group of Presbyterian families from the Laggan had better luck in 1684 and safely accomplished their voyage. Here and there, over the years individual families made the trip across the Atlantic Ocean.
James II was an ardent Catholic. He hated the Scots in general and the Presbyterians in particular. Between 1685 and 1688 James waged war on the Presbyterian Scots both in Scotland and in Ulster. In Ireland a complete overhaul of the army was King James' first order of business. The regiments which were primarily Protestant were disbanded and Catholic Irishmen were enlisted to replace them. Even the English soldiers were removed from the army. Then a native Irishman by the name of Tyrconnel was named to the position of general and given the directive to rid Ireland of all English and Scottish Protestants. These actions led hundreds of families to leave Ulster. But King James' reign of terror was short-lived; unable to convert the whole of the British Isles to Catholicism, he had abdicated the throne and fled to the safety of France. William of Orange landed on the shores of England in November of 1688 to make a bid for the throne. James had, by that time, raised a Catholic army in France and with it he journeyed to Ireland to join forces with General Tyrconnel's Irishmen. The combined army headed northward to attack the province of Ulster.
The Irish-French Catholic army laid siege to the town of Londonderry on 18 April, 1689. James expected the town to fall quickly, but it held out for 105 days. The timely arrival of supply ships and the formation of an army composed of local residents ended the siege and forced the Catholic army to retreat.
William of Orange's army crossed over to Ireland shortly after James' army retreated from Ulster. William led his army of ten thousand troops southward and confronted James' army near the Boyne River. The Battle of the Boyne took place during the 30th of June and the 1st of July, 1690 and ended in James' defeat. James promptly fled to France and William and his wife Mary assumed the throne of England. William granted freedom of worship to the Irish and permitted any of them that wished to go to France to do so. It is estimated that approximately eleven thousand took up the offer and eventually formed the Irish Brigade of the French Army.
Over the following fifty years more than 450,000 Irish migrated to France. Under William and Mary peace once more came to Ireland and Ulster began to prosper again. Most, if not all, of the native Irish families that had resided in the province of Ulster moved either southward or to France. Many of the families that had fled to Scotland began to return now and Ulster once more became predominantly Scottish.