Battle of Knocknaclashy Boyle had inspired a mutiny among the English Royalist garrison in Cork, causing them to defect to the Parliamentarians. This had outflanked the defences of Irish Confederates and English Royalists, causing them to retreat behind the river Shannon into Connacht, where they held the fortified cities of Limerick and Galway. Henry Ireton went on to besiege Limerick. The only organised Irish forces remaining in south Munster were those of Donagh MacCarthy, Viscount Muskerry, who held out in the mountainous area of west Cork and county Kerry – which was his clan’s native territory. In July 1651, Muskerry set out from
Cotter family his king, was made commander of the Jacobite forces in Cork. In 1691 Cotter was made Brigadier General in command of all the Jacobite forces in counties Cork, Kerry, Limerick and Tipperary. During the time of his authority Sir James Cotter treated the Protestant landowners well. He was rewarded for his moderation when, following the surrender of the Jacobite forces under the Treaty of Limerick, the support of his Protestant neighbours allowed him to retain his property and lands in full. Sir James Cotter was, in the style of previous generations of Irish chieftains, a great patron of poetry and