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But though Mary restored the Mass and re-asserted the jurisdiction of the Pope， her political policy in Ireland differed little from that of her father or her brother. She was as determined as had been Henry VIII. to bring the country under English law， and to increase thereby the resources of the Treasury. It is true that she allowed the young Garrett Fitzgerald， who had found a refuge in Rome， to return to the country， that she restored to him his estates and honoured him with a seat at the privy council. Brian O'Connor of Offaly was also released from prison and allowed to revisit his territories. During the time St. Leger held office he followed the old policy of strengthening English influence by conciliation rather than by force. But the Earl of Sussex was of a different mind. He marshalled his forces and made raids into the Irish districts， for the princes and inhabitants of which he entertained the most supreme contempt. It was during the reign of Mary that the plan of the English Plantations was first put into force by the removal of the native Irish from large portions of Leix and Offaly to make room for English settlers. And yet， in spite of the warlike expeditions of Sussex， the country went from bad to worse， so that Primate Dowdall could write to the privy council in England (1557) that "this poor realm was never in my remembrance in worse case than it is now， except the time only that O'Neill and O'Donnell invaded the English Pale and burned a great piece of it. The North is as far out of frame as it was before， for the Scots beareth as great rule as they do wish， not only in such lands as they did lately usurp， but also in Clandeboy. The O'Moores and O'Connors have destroyed and burned Leix and Offaly saving certain forts."[13]

On the death of Queen Mary in November 1558， her sister Elizabeth succeeded to the English throne. Although she had concealed carefully her Protestant sympathies， and had even professed her sincere attachment to the old religion during the reign of her predecessor， most people believed that important changes were pending. As soon as news of her proclamation reached Ireland early in December， the small knot of officials， who had fallen into disgrace during the reign of the late queen， hastened to offer their congratulations and to put forward their claims for preferment. Sir John Alen， formerly Lord Chancellor and Chief Commissioner for the dissolution of the monasteries， wrote to Cecil to express his joy at the latter's promotion， enclosed "a token，" and reminded him of what he (Alen) had suffered during the previous five years. Sir John Bagenall， ex-governor of Leix and Offaly， recalled the fact that he had lost heavily， and had been obliged to escape to France for resisting papal supremacy. He petitioned for a free farm worth ā50 a year. Bishop Staples， in a letter to Cecil， took pains to point out that he had been deprived of his See on account of his marriage， and had incurred the personal enmity of Cardinal Pole because he presumed to pray "for his old master's (Henry VIII.) soul."[14] For some time， however， no change was made， and Catholic worship continued even in Dublin as in the days of Queen Mary. The Lord Deputy Sussex went to England in December 1559， and entrusted the sword of state to the Archbishop of Dublin and Sir Henry Sidney， both of whom took the oath of office before the high altar in Christ's Church after Mass had been celebrated in their presence.

But the strong anti-Catholic policy of the new government soon made itself felt in England， and though the ministers were more guarded as far as Ireland was concerned， it was felt that something should be done there to lessen the influence of Rome. In the instructions issued to the Lord Deputy (July 1559) he was told that "the Deputy and Council shall set the service of Almighty God before their eyes， and the said Deputy and all others of that council， who be native born subjects of this realm of England， do use the rites and ceremonies which are by law appointed， at least in their own houses."[15] In the draft instructions as first prepared a further clause was added "that others native of that country be not otherwise moved to use the same than with their own contentment they shall be disposed， neither therein doth her Majesty mean to judge otherwise of them than well， and yet for the better example and edification of prayer in the Church， it shall be well done， if the said councillors being of that country born， shall at times convenient cause either in their own houses or in the churches the litany in the English tongue to be used with the reading of the epistle and gospel in the same tongue and the ten commandments."[16] Although Cecil struck out this clause with his own hand， it helps to show that the government feared to push things to extremes in Ireland.