The invasion of Ireland in 1649 was part of what we now call the English Civil War.
(Although it was actually a series of wars, and involved England, Scotland, Ireland and Wales.)
In 1641 - before the outbreak of war in Britain - there was a rebellion in Ireland, lead by the Irish Catholic aristocracy, to sieze control of the government from the mainly Protestant English & Scots ruling faction.
The rebels did well, and formed a ruling 'Confederation' with the Catholic clergy. By 1642, they controlled much of the country.
In 1642, war broke out in England between the King, Charles I, and parliament.
The Irish Confederation joined the Royalist side. (Charles was sympathetic towards the Catholic cause, whereas the Parliamentarians were staunch Protestants.)
They sent Irish troops to join the Royalist Armies in England, they fought against Parliamentarian forces in Ireland, & in 1644 they invaded Scotland.
But in Ireland, the leadership of the Confederation fell apart, arguing between themselves over whether to remain independent, or to submit to Royal command under King Charles.
It was a confusing situation: Pro-Royalist Confederates, Anti-Royalist Confederates, and English-led Parliamentarian forces all fought each other.
That was the situation in 1649, when the Parliamentarians finally won in England, executed the King, and established a Republic, under Oliver Cromwell.
Ireland was now the only part of the British Isles to remain at war. Cromwell himself led an invasion force to end the fighting once and for all. Over the next four years, 1649-53, the Parliamentary forces crushed all resistance and established their rule.
Although the campaign was undoubtedly brutal, it was very much the same as the rest of Britain had sufferred.
(For example, the massacre which followed the fall of Drogheda is often cited as an atrocity or war crime - but it was far less severe than the massacre which followed the fall of Newcastle, in England.)
Hope that helps!