With the outbreak of the Irish Rebellion of 1641, the local warlords, led by the O'Reillys, took control of the area. The O'Reillys "gave comfortable words to the Bishop" and Bedell's house at Kilmore in County Cavan was left untouched, becoming a place of refuge for those seeking shelter from the rebel insurgents. In the end, however, the rebels insisted upon the dismissal of all who had taken shelter in his house, and on the bishop's refusal he was seized and imprisoned with some others to the nearby island castle of Lough Oughter, Cloughoughter Castle.