Munster
In 1570 Perrot reluctantly accepted the newly-created post of Lord President of Munster in Ireland, a province in the throes of the first of the Desmond Rebellions. Perrot landed at Waterford in February of the following year and reduced the province to peace in a vigorous campaign.
The chief rebel, James Fitzmaurice Fitzgerald, eluded government forces for some time. In one grisly incident, after fifty rebels had been slain, Perrot sought to awe the rebels by cutting of the heads of the slain and fixing them to the market cross of Kilmallock. Fitzmaurice refused to come in and Perrot issued him with a challenge to single combat, which the rebel declined with the comment, "For if I should kill Sir John Perrot the Queen of England can send another president into this province; but if he do kill me there is none other to succeed me or to command as I do." Perrot's offer provoked mutterings from the more level-headed servants of the crown, and his reputation for rashness grew. Soon after, he was ambushed by the rebels, who outnumbered his force ten to one, but was relieved when the attackers fled on mistaking a small cavalry company for the advance party of a larger crown force. In 1572, after a second and successful siege of the Geraldine stronghold of Castlemaine, Perrot had the satisfaction of receiving Fitzmaurice's submission.
Perrot authorised over 800 hangings - most by martial law - but his presidency is regarded as successful. He criticised the reinstatement after the rebellion of the chief nobleman of Munster, Gerald Fitzgerald, 15th Earl of Desmond, and having vainly sought his own recall, departed Ireland without leave in July 1573. Upon presenting himself at court he was permitted to resign his office, in which he was succeeded by Sir William Drury.
Perrot returned to his Welsh home and occupied himself as vice-admiral of the Welsh seas and on the Council of the Marches. In 1578 the deputy-admiral, Richard Vaughan, accused him of tyranny, subversion of justice, and dealing with pirates; but Perrot retained the confidence of the Crown, for he became commissioner for piracy in Pembrokeshire in 1578, and in the following year received the command of a naval squadron charged with the interception of Spanish ships on the Irish coast.
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