Throughout the remainder of Queen Elizabeth's reign Catholics in England were not allowed to enjoy peace or respite. If priests, they were by that very fact liable to be hunted down and condemned as traitors; if they were laymen of substance, they were beggared by heavy fines imposed for non-attendance at the English service, or punished by imprisonment, and if they were too poor to pay a fine they could be driven from the kingdom for refusing to conform. Apart altogether from the immense sums levied on Catholics by fines and forfeitures, and from the number of people who died in prison either from confinement or torture, one hundred and eighty-nine were put to death for the faith under Elizabeth, one hundred and twenty-eight of whom were priests; and yet, notwithstanding this persecution, Catholics were still comparatively strong at the death of Elizabeth, and the supply of clergy showed no signs of being exhausted. Over three hundred and sixty priests were in England attending to the wants of their co-religionists in 1603.
Unfortunately the dissensions among the Catholic party in England and on the Continent did more harm to their cause than Elizabeth's persecutions. The close co-operation of Allen and Persons with Spanish political designs for the overthrow of Elizabeth and the invasion of England was as distasteful to a large body of the lay Catholics in England as it was to many of the clergy.[39] Though serious disputes had broken out long before, it was only after the death of Cardinal Allen in 1594 that the crisis reached a head. Many of the secular clergy objected warmly to the influence of the Jesuits, and ugly controversies broke out in England and in the English colleges abroad.
Persons and his friends were supposed to be plotting in favour of the succession of a Catholic to the throne on the death of Elizabeth, while most of their opponents favoured the succession of James VI. of Scotland, from whom they expected at least toleration. To put an end to what the latter regarded as the excessive authority of the Jesuits they insisted on the appointment of a bishop who would take charge of English affairs, but for various reasons the Holy See refused to yield to their request. As a compromise, however, George Blackwell was appointed archpriest (1598) with secret instructions, it was said, to consult Garnet, the Jesuit superior in England. The selection was singularly unfortunate, as neither from the point of view of prudence nor of reliability was Blackwell fitted for the extremely delicate position which he was called upon to fill. The seculars refused at first to obey his authority and appealed again to the Pope, who confirmed the appointment. As many of the seculars were still unwilling to yield some of the leaders were censured by the archpriest. A new appeal was forwarded to Rome. In 1602 Clement VIII.
issued a document upholding the authority of the archpriest, and, while firmly defending the Jesuits against the charges that had been made against them, warned Blackwell that he should not take his instructions from any person except from the Pope or the Cardinal Protector of England.[40] This controversy could not be kept a secret.
It was known to the entire Catholic body, and it was used with great force and success by their opponents. The government took sides with the secular clergy and offered them facilities for carrying their appeals to Rome, but news of the secret negotiations between the seculars and the authorities having been divulged Elizabeth issued a new proclamation (1602) in which she announced that she had never any intention of tolerating two religions in England.[41] The Jesuits and their adherents were commanded to quit the kingdom within thirty days, and their opponents within three months under penalty of treason. To give effect to this proclamation a new commission with extraordinary powers was appointed to secure the banishment of the Catholic clergy.