These successes synchronize exactly with the expectation of a second Spanish Armada, which filled Elizabeth with her old apprehensions. Philip was persuaded again to tempt the fortune of the seas, and towards the end of October his fleet, under the Adelantado of Castille, appeared off the Scilly Islands, with a view to secure the Isle of Wight, or some other station, from which to operate an invasion the ensuing spring. Extraordinary means were taken for defence; the English troops in France were recalled, new levies raised, and the Queen's favourite, the young Earl of Essex, appointed to command the fleet, with Raleigh and Lord Thomas Howard as Vice-Admirals. But the elements again fought for the northern island; a storm, which swept the channel for weeks, drove the English ships into their ports, but scattered those of Spain over the Bay of Biscay. In this second expedition sailed Florence Conroy, and other Irish exiles, who had maintained for years a close correspondence with the Catholic leaders. Their presence in the fleet, the existence of the correspondence, and the progress of the revolt itself, will sufficiently account for the apparent vacillations of English policy in Ulster in the last months of 1597. Shortly before Christmas, Ormond, now Lord Lieutenant, accompanied by the Earl of Thomond, attended only by their personal followers, visited Dungannon, and remained three days in conference with O'Neil and O'Donnell. The Irish chiefs reiterated their old demands: freedom of worship, and the retention of the substantial power attached to their ancient rank. They would admit Sheriffs, if they were chosen from among natives of their counties, but they declined to give hostages out of their own families. These terms were referred to the Queen's consideration, who, after much protocoling to and fro, finally ratified them the following April, and affixed the great seal to O'Neil's pardon. But Tyrone, guided by intelligence received from Spain or England, or both, evaded the royal messenger charged to deliver him that instrument, and as the late truce expired the first week of June, devoted himself anew to military preparations.
In the month of June, 1598, the Council at Dublin were in a state of fearful perplexity. O'Neil, two days after the expiration of the truce, invested the fort on the Blackwater, and seemed resolved to reduce it, if not by force, by famine. O'Donnell, as usual, was operating on the side of Connaught, where he had brought back O'Ruarc, O'Conor Sligo, and McDermot, to the Confederacy, from which they had been for a season estranged. Tyrrell and O'Moore, leading spirits in the midland counties were ravaging Ormond's palatinate of Tipperary almost without opposition. An English reinforcement, debarked at Dungarvan, was attacked on its march towards Dublin, and lost 400 men. In this emergency, before which even the iron nerve of Ormond quailed, the Council took the resolution of ordering one moiety of the Queen's troops under Ormond to march south against Tyrrell and O'Moore; the other under Marshal Bagnal, to proceed northward to the relief of the Blackwater fort. Ormond's campaign was brief and inglorious. After suffering a severe check in Leix, he shut himself up in Kilkenny, where he heard of the disastrous fate of Bagnal's expedition.