In 1570, Magrath was appointed by
the Crown as the Protestant
Bishop of Clogher, including the
temporalities, and visited England, where he fell ill of a fever. In February 1571, he was then appointed
Archbishop of Cashel and
Bishop of Emly (no new appointment was made to Clogher until 1605). In the same year he imprisoned some Franciscan priests at Cashel. In a rage, the rebel crusader
James Fitzmaurice Fitzgerald threatened to burn to ashes everyone and everything connected with
Archbishop Magrath if they were not released. The friars were immediately liberated by Edward Butler. In 1572 Magrath brought charges against Butler's elder brother,
The 10th Earl of Ormonde, but they were given no credence. In 1575, as he went on his way to Dublin, he was attacked and badly injured by the
kerne of a hostile clan. Until the end of the
Desmond Rebellions in 1583, Magrath remained in his province, while assisting the English government on the one hand and intriguing with the Catholic rebels on the other. In October 1582, he travelled to England bearing letters of strong recommendation, which cited his ability to provide valuable information on the rebels. He complained that Cashel was only worth £98 and – in spite of the misgivings of
William Cecil, Lord Burghley – was granted the See of
Waterford and Lismore in commendam, which he held until 1589, and then again from 1592 upon the death of Bishop Wetherhead. Despite his allegiance to the authorities, Magrath never arrested the new Catholic Archbishop of Cashel, Dr Kearney, who lived peacefully under his nose. However, Magrath continued to court favour with the authorities, and in 1584 he did arrest the Catholic
Bishop of Emly,
Maurice MacBrien, who died two years later in custody in
Dublin Castle. In March 1589 he wrote commending the Kerry plantation undertaker
Sir William Herbert, who was a controversial figure on the Protestant side. In 1591 Magrath visited England without leave, and grave charges were pressed against him in his absence. During his visit he sought to convert to Protestantism the condemned Gaelic Prince of
Breifne,
Brian O'Rourke, who scorned the bishop at the foot of the gallows-ladder before his execution in London. At about this time Magrath's cousin,
Dermot Creagh, was the Catholic
Bishop of Cork and Cloyne with Legatine authority in
Munster, and they remained on mutual terms. Magrath appears to have feared that his soul was in jeopardy, and with a view to repentance and reconciliation with Rome, took care that his cousin would not be captured, while at the same time feeding information to the Crown about his whereabouts. ==Nine Years War==