He therefore, kept aloof during the Desmond Rebellions, but during Sir George Carew's victorious march through Limerick after he had taken the Castle of Lough Gur, he was called upon to submit to Queen Elizabeth.
He did not feel happy under the "protection" of the Queen and applied for leave to travel to Spain on a "pilgrimage to St. Iago", but this was refused him and he was compelled to remain with his family at Brittas.
During the short lull in the persecutions he openly attended Divine Service at St. Mary's Cathedral, temporarily restored to the Catholics, and was received together with his family and retainers, into the Dominican Confraternity of the Holy Rosary.
Again the good offices of Sir George Thornton obtained his release, but although restored to his estates and fortune, he continued to harbour the hunted priests and was acknowledged "protector of the Catholics".
In October 1607, while Mass was being celebrated in Brittas Castle, he was betrayed by his kinsmen, Theobald Bourke of Castleconnell and Sir Edmond Walsh of Abington.