Why are we asking this now?

The 350th anniversary of Oliver Cromwell's death last week was marked by the publication of a new book which suggests that the Lord Protector of England's reputation should be reassessed in the light of two massacres he conducted in Ireland. The slaughter at Drogheda and Wexford in 1649 rank among the greatest atrocities in Anglo-Irish history, suggests the historian Micheál Ó Siochrú in God's Executioner: Oliver Cromwell and the Conquest of Ireland. England's great parliamentarian, he says, was guilty of war crimes, religious persecution and ethnic cleansing.

Not what British readers are used to, eh?

In recent years, that's true. The overwhelming majority of the 150 biographies of Cromwell published over the past century have been favourable. And Cromwell came third in a BBC poll to find the greatest Briton of the second millennium. But in Ireland we have long taken a different view. Cromwell has also viscerally divided thinkers in the past. David Hume dubbed him the "most frantic enthusiast... most dangerous of hypocrites... who was enabled after multiplied deceits to cover, under a tempest of passion, all his crooked schemes and profound artifices".

He has even been called the father of European fascism. But admirers like Thomas Carlyle painted him as a hero in the battle between good and evil – a man who restored morality in an age dominated by expediency and compromise, who pressed a new political equality and a religious toleration which extended to readmitting the Jews to England 350 years after they had all been expelled.

What took Cromwell to Ireland?

In 1641, Irish Catholics attacked the Protestant settler community. Thousands were killed. But news of atrocities were greatly exaggerated in the English press, which reported that as many as 200,000 had been slaughtered. Cromwell, then an obscure MP, served on a committee to organise relief for the Protestant victims. Within a decade, he had become, thanks to the English Civil War, the greatest soldier of the era, and when a new rebellion occurred in Ireland against the Parliament which had overthrown the English king, his response was governed by the outrage he still harboured at the earlier atrocity.

What did he do here?

The first major town Cromwell encountered was Drogheda. He summoned the royalist commander and invited him to surrender. When he refused, Cromwell's model army seized the town and put the entire garrison of 2,500 officers and men to the sword. It was an act of ruthlessness which sent shockwaves of fear through the rest of Ireland. Other towns surrendered as soon as Cromwell's army approached, and their inmates were spared.

Only Wexford refused. During the siege there, Parliamentarian troops broke into the town while negotiations for its surrender were ongoing, killing about 2,000 soldiers and 1,500 townspeople.

Wasn't that how wars were fought then?

Historians disagree on that. Some, like Tom Reilly in Cromwell, an Honourable Enemy, suggest what happened at Drogheda was not unusually severe by the standards of 17th-century siege warfare. Other historians, like Ó Siochrú, suggest that Cromwell's resort to extreme violence was not a reaction to the conditions of battle but a pre-determined exercise in religious and ethnic vengeance.

Could he have acted differently?

Probably. He had arrived in Ireland in a strong position politically; Charles I had been executed, the mutiny of the Leveller radicals had been crushed, and the Commonwealth declared. Militarily, he was dominant too; he had an effective and disciplined army and the opposition was what the poet Milton described as "a mixed rabble, part papists, part fugitives, and part savages". He ought to have been able to pacify Catholic Ireland with minimal violence. On the other hand, more than 80% of Ireland was in the hands of those hostile to the Parliamentarian's revolution. There were fears that a force from Ireland might invade England and threaten the settlement which Parliament had established in its victory over the king.

What is the case for the defence?

That Cromwell was just a man of his time. What he did in the two sieges was in accordance with well-established military practice. That his decision to make an example of the garrisons at Drogheda and Wexford was intended to prevent more extensive bloodshed throughout the land. That the civilians killed were, in modern parlance, unhappy collateral damage. That compared to others, he was one of the most restrained of all the commanders in Ireland in the early modern period. And that he cannot be held accountable for what happened in Ireland after he had gone.

What happened after he left?

Cromwell's forces ordered Irish Catholics to move and live west of the Shannon. The alternative to this forced mass population transfer was clear. Catholics were told "To Hell or to Connaught!" It was the greatest act of ethnic cleansing in Ireland or Britain since the Norman Conquest. By the end of 1656, four-fifths of the land was in Protestant hands. When Catholics fought back, in guerrilla groups numbering some 30,000, Cromwell's generals forcibly evicted civilians who were thought to be helping the resisters and systematically burned the area's crops and killed all livestock.

So what's the overall verdict?

Cromwell was a paradox. He was a great Englishman who swept away the last remnants of feudalism from his land, paving the way for democracy, freedom and tolerance. But the drive and idealism which motivated him to do that were perverted into a ruthless dismissal of the humanity of those who were his political and religious opponents. Drogheda and Wexford were his Hiroshima and Nagasaki. The question of whether evil can be done in the name of good is not one which was peculiar to him or to his time.

Hidden History, RTE1, Tuesday, 10.15pm