His first step was to recall the Duke of Ormond, whom Charles had left as Viceroy, and to appoint in his place two Lords Justices, Lord Granard and the Primate Boyle, who were likely, he believed, to be more malleable.  All tests were to be immediately done away with.  Catholicism was no longer to be a disqualification for office, and Roman Catholics were to be appointed as judges.  A more important change still, the army was to be entirely remodelled; Protestant officers were to be summarily dismissed, and Roman Catholic ones as summarily put in their places.

Such sweeping changes could not, even James found, be carried out all at once.  The Lords Justices were next dismissed, and his own brother-in-law, Lord Clarendon, sent over as Lord-Lieutenant.  He in turn proving too timid, or too constitutional, his place was before long filled by Richard Talbot, a fervent Catholic, but a man of indifferent public honour and more than indifferent private character.  Talbot was created Earl of Tyrconnel, and arrived in 1686 avowedly to carry out the new policy.

From this point the stream ran fast and strong.  The recent innovations, especially the re-organization of the army, had naturally caused immense alarm amongst the whole Protestant colony.  A petition drawn out by the former proprietors and forwarded to the king against the Act of Settlement had made them tremble also for their estates, and now this new appointment came to put a climax to their dismay.  What might not be expected they asked in terror, under a man so unscrupulous and so bigoted, with an army, too, composed mainly of Roman Catholics at his back to enforce his orders?  The departure of Clarendon was thus the signal for a new Protestant exodus.  Wild reports of a general massacre, one which was to surpass the massacre of ’41, flew through the land.  Terrified people flocked to the sea-coast and embarked in any boat they could find for England.  Those that remained behind drew themselves together for their own defence within barricaded houses, and in the towns in the north, especially in Enniskillen and Londonderry, the Protestant inhabitants closed their gates and made ready to withstand a siege.

Meanwhile in Dublin sentences of outlawry were fast being reversed, and the estates of the Protestants being restored in all directions to their former proprietors.  The charters of the corporate towns were next revoked, and new (by preference Catholic) aldermen and mayors appointed by the viceroy.  All Protestants were ordered to give up their arms by a certain day, and to those who did not, “their lives and goods,” it was announced, “should be at the mercy and discretion of the soldiers.”  These soldiers, now almost exclusively Catholic, lived at free quarters upon the farms and estates of the Protestants.  “Tories,” lately out “upon their keeping,” with prices upon their heads, were now officers in the king’s service.  The property of Protestants was seized all over the country, their houses taken possession of, their sheep and cattle slaughtered by hundreds of thousands.  All who could manage to escape made for the north, where the best Protestant manhood of the country had now gathered together, and was standing resolutely in an attitude of self-defence.