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This controversy arose in England on the appointment of George Blackwell as archpriest with jurisdiction over the secular clergy of England and Scotland, by the Holy See on 7 March, 1598. The last member of the ancient hierarchy, Goldwell, Bishop of St. Asaph's , had died in 1585, and thenceforth Cardinal Allen exercised informal jurisdiction with the acquiescence of the pope and by common consent of the missionary priests, then numbering about three hundred. After Allen's death in 1594 the want of a superior made itself felt. For some years there had been trouble at the English College in Rome, resulting in difficulties between the Jesuits and the secular clergy, which were accentuated by the dissensions among the priests imprisoned at Wisbech. In 1597 Father Persons, who had general charge of the Jesuit mission in England, went to Rome, where the troubles at the English College had come to a head, and settled matters by becoming rector there himself. Some of the secular clergy, resenting the growing influence of the Society in the affairs of the English Catholics and distrusting the political views of Father Persons, drew up a memorial against the Jesuits to be presented to the pope. Others wished for concord with the Jesuits, and believed that the true solution of difficulties so deeply prejudicial to Catholic interests in England lay in the appointment of a bishop. Persons himself at first favoured the appointment of one or more bishops, preferably one to live and work in England and another to live in the Low Countries so as to organize and direct affairs while free from personal danger. But this plan was given up, the appointment of an archpriest being decided on and effected by Cardinal Cajetan, Cardinal-Protector of England. This absolutely new form of ecclesiastical government was actively resented by a small but influential body of secular priests, who claimed that they had the sympathy of a larger number of their brethren. Two of them, William Bishop and Robert Charnock, were sent to Rome to dispute the validity of the appointment and to explain their grievances, but on their arrival in December, 1598, they were arrested and confined as prisoners in the English College. On 6 April, 1599, a Brief was issued confirming the appointment of the archpriest, and the imprisoned priests were released and dismissed from Rome, but forbidden to return to England. In England Thomas Lister , a Jesuit, charged the appellant priests with schism, in a pamphlet which stirred up a controversy in which both sides employed unmeasured and violent language.

Though the Brief confirming the archpriest was at once accepted by the secular clergy, Blackwell insisted that the appellant priests should make reparation for the guilt of schism. They denied that they were guilty of schism in appealing to the pope, and referred the question to the University of Paris, which decided in their favour. Blackwell issued a decree condemning this judgment, and renewed another decree which he had published in the previous January, forbidding the publication of any defence of the appellants' conduct under pain of suspension. On 17 November a formal appeal to Rome was signed by thirty-three priests. This they supported by various pamphlets, which had been published early in 1601. The English Government now knew of the trouble, and the Protestant Bishop of London entered into negotiations with Bluet, one of the imprisoned priests, with the result that Bluet was brought before the Privy Council and induced them to "banish" four of the appellant priests that they might prosecute their appeal. Bagshaw, Champney, Bluet, and Barneby were chosen, but finally Mush and Cecil took the places of Bagshaw and Barneby. Bagshaw published a violent work called the "True Relation", and Watson, a priest, issued extravagant tirades against Blackwell and the Jesuits. On 26 January, 1602, Blackwell published a Brief dated 17 August, 1601, which had been in his possession since Michaelmas. This again confirmed the appointment, but condemned the archpriest's irritating conduct, suppressed all publications about the controversy, refused to admit any appeal, and urged mutual charity.

In Rome, however, the appellants succeeded with the help of the French ambassador in gaining a hearing, and on 5 October, 1602, a new Brief was issued (text in Tierney, op. cit. infra, III, clxxxi) which Tierney summarizes as "condemning the conduct of the archpriest, and justifying the appellants from the charges of schism and rebellion, which had been urged against them. . . . It limited his jurisdiction to the priests educated in the foreign seminaries ; forbade him, in future and for the sake of peace, to communicate either with the superior of the Jesuits in England, or with the general of the Society in Rome on the concerns of his office; commanded him to supply the first three vacancies that should occur in the number of his assistants with persons selected from amongst the appellant priests, and having ordered him to receive and transmit all appeals to the Cardinal Protector , concluded by condemning the past, and prohibiting all future publications in any manner connected with the present controversy". On the other hand the appellants failed to secure episcopal government, or the prohibition, which they sought, to restrain priests, whether secular or regular, from provoking the Government by interference in political affairs. Nor did they obtain their request that all Catholics should be bound to manifest any designs against the queen or State of which they should learn. Elizabeth and her ministers were disappointed at the tenor of the Brief and retaliated by a proclamation (5 November, 1602) for the banishment of all Catholic missionaries. In reply to this thirteen of the appellants, including two future martyrs, drew up their famous address to the queen assuring her of their loyalty. (See Tierney, op. cit. infra, III, 55-56, and clxxxviii sqq.) The papal Brief of 5 October, 1602, finally settled the question, but an unfortunate legacy of mutual distrust and sore feeling remained behind and embittered the relations of the parties for many years to come. Government by archpriest never worked well, and the secular clergy became unanimous in their desire for a bishop. This was granted to them after the death of William Harrison, the third archpriest, in 1621, when the Holy See selected William Bishop, one of the leading appellants, to be the first Vicar Apostolic of England.

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