[10] Naunton claimed Sir Owen Hopton, Lieutenant of the Tower of London, overheard Perrot say, "Will the Queen suffer her brother to be offered up as a sacrifice to the envy of his frisking adversaries?

He served as member of parliament for Carmarthenshire in 1547, Sandwich in 1553 and 1555, Wareham in 1559 (presumably through pressure exerted on the Rogers family by the 2nd Earl of Bedford, his former commander[14]), Pembrokeshire in 1563, and Haverfordwest in 1589.

[15] In 1570 Perrot reluctantly accepted the newly created post of Lord President of the Irish province of Munster, which was in the throes of the first of the Desmond Rebellions.

[4] In one grisly incident, after fifty rebels had been slain, Perrot sought to awe his enemy by cutting off the heads of the corpses and fixing them to the market cross of Kilmallock.

[4] Before he had time to begin in the south, Perrot got wind of raids into the northern province of Ulster by the Scottish clans Maclean and MacDonald in alliance with Somhairle Buidhe Mac Domhnaill.

Perrot marched a contingent of the Royal Irish Army north from the Pale to confront the Scots, but Sorley Boy evaded them by retreating to Scotland, only to return later with reinforcements.

Elizabeth roundly abused her deputy for launching such an expensive and unadvised campaign, but by 1586 Perrot had brought Sorley Boy to a mutually beneficial submission.

[4] At about this time Perrot also sanctioned the kidnapping at Rathmullan of Hugh Roe O'Donnell, Tanist to the Chief of the Name of Clan O'Donnell, (who was lured to a wine tasting on a merchant ship anchored in Lough Swilly and then sealed in a cabin and brought to imprisonment in Dublin Castle), a move which gave the crown some leverage over the Irish clans of County Donegal.

In the west, Perrot did have success in 1585 by perfecting a composition of the province of Connaught, an unusually even-handed contract between the Crown and landowners by which the Queen received certain rents in return for settling land titles and tenant dues.

The sessions proved a disappointment: although the act for the attainder of Desmond (clearing the escheat of the rebel's estates to the Crown) was passed, the ambitious schedule of legislation ran into difficulty, particularly over the suspension of Poynings' Law.

At the prorogation in 1587, Perrot was so frustrated with the influence of factions within both houses of parliament (orchestrated to a large degree by the Earl of Ormond) that he begged to be recalled to England.

His plan for the conversion of the revenues of St. Patrick's Cathedral to fund two colleges led to a sustained quarrel with the Archbishop of Dublin, Adam Loftus, whom Perrot wilfully aggravated by his interference with the prelate's secular authority as Lord Chancellor.

In the heated politics following the defeat of the Spanish Armada he was accused of treason,[4] based on allegations made in Ireland by a former priest and condemned prisoner, Sir Dennis O'Roghan.

[citation needed] The evidence was provided in letters allegedly addressed by Perrot as Lord Deputy (with his signature attached) to King Philip II of Spain and the Duke of Parma, in which certain treasonable promises were made on the future dominion of England, Wales and Ireland.

[citation needed] Fitzwilliam started an investigation into the charges in Dublin, but O'Roghan's record of forging documents was quickly produced, and for a time it seemed the allegations would fail for lack of credible evidence.

[citation needed] O'Roghan alleged that he had been tortured by members of this commission, and Fitzwilliam was instantly directed on strict instruction from the Queen to resume his original investigation and forward the findings to the Privy Council in London.

Perrot faced a moment of crisis when further allegations were made – most notably by his former secretary, Henry Bird – of his frequent use in private conversation of violent language against the Queen.

He was also accused of having prior knowledge of the rebellion in 1589 of Sir Brian O'Rourke (later extradited from Scotland and hanged at London), which had occurred under the government of Bingham in Connaught.

[5] Following Perrot's imprisonment, some of his Irish favourites had been replaced in their council seats by English appointees, who fully equated Protestantism with the state and were inclined towards total war against Gaelic Ireland.

Fitzwilliam felt free to pursue a policy opposed in crucial aspects to Perrot's, and the Irish clan chiefs of Ulster (including Hugh O'Neill) suffered increasing evictions of their clansmen and Protestant Plantation upon their territories, which helped trigger the outbreak of the Nine Years War (1595–1603).