The execution of
Charles I in 1649 led local Protestant and Scottish forces in
Ulster to join the Duke of Ormond's royalist coalition, thus isolating Coote. He defended
Derry against a protracted siege (March–August 1649), with the unlikely assistance of the
Irish Confederate Ulster army under
Owen Roe O'Neill. After the
New Model Army under
Cromwell captured
Drogheda, a detachment under
Robert Venables headed north into Ulster, where Coote joined Venables to destroy the Scottish Ulster Royalists at the
Battle of Lisnagarvey. By early 1650, however, the Irish Ulster army (now under
Heber MacMahon, as O'Neill had died a few months earlier) became active once more, and Coote was again forced onto the defensive. After being reinforced, he advanced on the Irish army at
Scarrifholis and routed them, killing over 2,000 soldiers and taking no prisoners. After this, Coote's army
attempted to take the formidable fortress of
Charlemont, which was defended by the remnants of the Ulster army, but his soldiers suffered heavy casualties before the stronghold surrendered. With Ulster largely cleared, in June 1651, Coote advanced on
Athlone from the north-west, evading a blocking force. Through this movement the town was gained; the town contained a stone bridge over the Shannon and this action thus opened up
Connacht to the Parliamentarian army for the first time. Having entered Connacht, Coote laid siege to Galey Castle, the seat of the
Ó Ceallaigh clan. The Ó Ceallaighs resisted, and for their defiance, they were taken to An Creagán (a local stoney, stepped hill), and were hanged. The hill thereafter came to be known as 'Cnoc an Chrochaire', 'the Hill of the Hanging', and gave its name to the adjacent village, now Anglicised as ‘
Knockcroghery’. Coote continued westwards and besieged
Galway in the winter of 1652. Galway surrendered in April 1652. Coote inherited the substantial plantation lands of his father in the midlands of Ireland. ==Restoration==