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The negotiations for the marriage of Prince Charles to a Spanish princess made it necessary for the king to be more guarded in his religious policy in Ireland. Oliver St. John, who had shown himself to be such a bitter enemy of the Catholics, was removed from office, and Lord Falkland was sent over as Deputy in 1622. Rumours were afloat on all sides that his policy was to be one of toleration. The Protestants were alarmed and at the installation of the new Deputy (Sept. 1622)James Ussher, then Protestant Bishop of Meath, taking as his text, "He beareth not the sword in vain," preached a violent sermon in favour of religious persecution. Primate Hampton wrote immediately to the preacher, reproving him for his imprudence, asking him to explain away what he had said about the sword, and advising him to spend more of his time in his own diocese of Meath, where matters were far from being satisfactory.[34] On the return of Charles from Spain a new proclamation was issued (1624) ordering all "titulary popish archbishops, bishops, vicars-general, abbots, priors, deans, Jesuits, friars, seminary priests, and others of that sect, made or ordained by authority derived from the See of Rome or other foreign parts to depart from the kingdom within forty days under pain of his Majesty's indignation and penalties. If any of these dared to remain, or if any persons dared to receive them, the offenders were to be lodged in prison, "to the end such further order may be taken for their punishment as by us shall be thought fit."[35]

A full account of the position of the Catholics of Ireland is given in a letter written from Dublin in 1623. Catholic minors were compelled to accept the oath of supremacy before they could get letters of freedom from the Court of Wards (established 1617); all mayors, magistrates, officials, etc., of corporate towns were commanded to take the oath under penalty of having their towns disenfranchised;priests were arrested and kept in prison; laymen were punished by sentences of excommunication and by fines for non-attendance at Protestant worship; they were summoned before the consistorial courts for having had their children baptised by the priests and were punished with the greatest indignities; Catholics were forbidden to teach school and Catholic parents were forbidden to send their children abroad; the Catholic inhabitants of Drogheda were indicted before a Protestant jury, and having been found guilty of recusancy, they stood in danger of having all their property forfeited; in Louth the juries were ordered to draw up a list of Recusants; when three Catholic jurors refused they were thrown into prison and obliged to give security to appear before the Dublin Star Chamber; and in Cavan proceedings of a similar kind were taken.[36]

Amongst the distinguished bishops of the Irish Church at this period were Peter Lombard, Archbishop of Armagh (1601-25), a native of Waterford, who studied at Oxford and Louvain, was appointed a professor at the latter seat of learning, took a very prominent part in the /Congregatio de Auxiliis/, published some theological treatises together with an ecclesiastical history of Ireland, entitled, /De Regno Hiberniae, Sanctorum insula, Commentarius/,[37] but who on account of the danger of stirring up still greater persecution never visited his diocese; Eugene Matthews or MacMahon, Bishop of Clogher (1609) and Archbishop of Dublin (1611) who did splendid work for the Irish Church by the decrees passed in the provincial synod at Kilkenny (1614) as well as by his successful efforts for the foundation of the Pastoral College at Louvain; David O'Kearney, appointed to Cashel (1603) as successor to the martyred Archbishop O'Hurley, who though hunted from place to place continued to fill the duties of his office till about the year 1618, when he went to Rome; and Florence Conry, Archbishop of Tuam, a Franciscan, who served with the army of the Northern Princes, and who was specially detested by the English government on account of his loyal defence of O'Neill. Not being allowed to return to Ireland, he devoted himself to the study of theology, and was the author of several very important works, some of which were not, however, free from the suspicion of something akin to Jansenism. By far the most useful book he composed was his celebrated Irish Catechism published at Louvain in 1626.[38]