Oliver Cromwell was a snake and gave no one his mercy. He and his troops enthusiastically slaughtered the Irish people and destroyed everything in their path. He would rather kill the Irish than even lay eyes on them - and he did. He and his troops ravaged and devastated the land. Defenseless people (men, women and children) were murdered by the scores with absolutely no regard whatsoever. Basically, if you were in his path you were a goner. In one of his most callous acts he burned hundreds of people alive. Hearing that Cromwell was advancing to their area the people in reign around the Rock of Cashel flocked there for refuge. When Cromwell arrived they went into the church in the hope of being spared. Instead Cromwell ordered his men to barricade them inside. They then piled turf all around the church and set it ablaze. If you travel to Ireland you will see many ruins. You can thank Cromwell and his troops for many of them.
Now that the country was in ruins and under complete control of the Crown the Plantation of Ulster could commence. The millions of acres of land that had been confiscated were given to loyal subjects of the Crown (mostly Scottish Presbyterians) who immigrated to Ireland. These people were and remain separatists. The plantation process has caused terrible internal strife in Ireland, which remains to this very day.
The English then initiated a series of unjust laws to further crush the Irish people - the dreaded Penal Laws. In essence, you were penalized for being Catholic. During this time a new parliament was established in Dublin. Every representative was a Protestant. The Irish Catholics had no rights or representation. Under the Penal Laws, Catholics could not practice their faith, hold office, carry weapons, teach school, purchase or lease land, marry a Protestant, work at any scientific endeavor or own a horse worth more than five pounds. If you were lucky enough to be a Catholic horse owner and a Protestant approached you with an offer to buy your horse for the sum of five pounds you had to sell. If you refused you would be executed.
In 1685 King Charles II died. Upon his death his brother James ascended to the throne to become the King of England. James, oddly enough, was a Catholic. He looked upon the Irish people with favor. Obviously, this did not sit very well with many in the English hierarchy. In addition, the Protestants in Ireland were becoming increasingly uneasy over the situation. It was not long before James was met with an opponent, William of Orange. James did not have much support in England (or much of an army either). Therefore, he felt his best chances to win the battle against William was to fight in Ireland. He knew he could count on the support of the Irish. However, his army (and the Irish) lacked training and weapons. In 1690 he met William in the Battle of the Boyne and was defeated. The Crown was once again firmly in the hands of the Protestants.