In the autumn of
1567 Sidney returned to England, and was absent from Ireland for the next ten months. On his return he urged upon
Cecil the necessity for measures to improve the economic condition of Ireland, to open up the country by the construction of roads and bridges, to replace the Ulster tribal institutions by a system of freehold land tenure, and to repress the ceaseless disorder prevalent in every part of the island. In 1569, he oversaw the opening of parliament, the first to be held for ten years.
In pursuance of this policy Sidney proposed the appointment of a military governor ("Lord President") in the provinces of
Munster and
Connaught. This provoked the first of the
Desmond Rebellions led by
James Fitzmaurice Fitzgerald of the Geraldine family, which had been put down with great severity by 1573. Sidney also dealt severely with the unruly Butlers in Ormond and Kilkenny, who had risen out in defiance of the government in reaction to the opportunistic claims to certain of their lands by Sir
Peter Carew, a rather rough gentleman from Devon who pursued his entitlement with the blessing of the Dublin administration. At
Kilkenny large numbers of Sir Edmund Butler's followers were hanged, and three brothers of
Thomas Butler, 3rd Earl of Ormonde, were attainted by an act of the
Irish parliament in 1570.
Sidney left Ireland in
1571, aggrieved by the slight appreciation of his statesmanship shown by the queen; but he returned thither in September, 1575 with increased powers and renewed tokens of royal approval, to find matters in a worse state than before, especially in Antrim, where the
MacQuillans of the Route and
Sorley Boy MacDonnell were the chief fomenters of disorder. Having to some extent pacified this northern territory, Sidney repaired to the south, where he was equally successful in making his authority respected. He left his mark on the administrative areas of the island by perfecting certain shire divisions on the English model.
At an earlier period he had already in the north combined the districts of the Ardes and Clandeboye to form the county of Carrickfergus, and had converted the country of the O'Farrells into the county of Longford; he now carried out a similar policy in Connaught, where the ancient Irish district of
Thomond became the
county Clare, and the counties of
Galway, Mayo, Sligo and
Roscommon were also delimited.
Sidney also suppressed a rebellion headed by the earl of Clanricarde and his sons in 1576, and hunted Rory O'More to his death two years later. Meantime Sidney's annual levy (the cess), which was designed to fund a central government militia, had caused discontent among the gentry of
the Pale, who carried their grievances to queen Elizabeth. Greatly to Sidney's chagrin the queen censured his extravagance, and notwithstanding his distinguished services to the Crown he was recalled in September 1578, and was coldly received by Elizabeth.