In 1645 a new papal nuncio landed in Ireland with arms and funds to support the rebellion and befriended MacEgan, appointing him chaplain general of the Ulster forces.
In 1646 he was proposed as bishop of Ross by the nuncio himself and consecrated at Waterford in 1648, but probably never gained access to his see, which remained under Protestant control.
On Cromwell's landing in 1649, MacEgan became very active in rallying the Confederation forces and organising defensive measures.
He then joined David Roche's force of untrained men who were intending to relieve the siege of Clonmel.
MacEgan himself was captured and taken the following day to the walls of Carrigadrohid castle, which was occupied by Confederation forces, and told to call on them to surrender.