Dr Allen had left England in 1561, and taken refuge in Belgium, but he returned in the following year, and went around among the persecuted Catholics, exhorting them to be steadfast in their Faith. He found that the people were not Protestants by choice, and he was convinced that all they needed was an organized body of trained men to look after their spiritual needs, to comfort them in their trials, and to keep them well-instructed in their religion. Because of the lack of such help they were not only becoming indifferent, but were almost ready to compromise with their persecutors. Henry had confiscated ninety colleges, two thousand three hundred and fourteen chantries and free chapels and ten hospitals, besides putting to death seventy-six priests and monks, beginning with Fisher, the Bishop of Rochester, as well as a great number of others, gentle and simple, conspicuous among whom was the illustrious chancellor, Thomas More. There was a partial cessation of persecution when Edward VI, a boy, was placed on the throne, and, of course, the conditions changed completely when Mary Tudor came to her own. But when the terrible Elizabeth, infuriated by her excommunication, took the reins of government in her hands, no one was safe. Unfortunately, however, in the interval, the people had become used to the situation, and it began to be a common thing for them to resort to all sorts of subterfuges, even going to Protestant churches to conceal their Faith. Hence, there was great danger that, in the very near future, Catholicity would completely die out in England. Allen proposed to Father Mercurian to employ the Society to avert that disaster.
Some of the General's consultors balked at the project because it implied an absolutely novel condition of missionary life. There were none of the community helps, such as were available even in the Indies and in Japan; for, in England, the priest would have to go about as a peddler, or a soldier, or a sailor, or the like, mingling with all sorts of people, in all sorts of surroundings, and would thus be in danger of losing his religious spirit. The obvious reply was that if a man neglected what helps were at hand he would no doubt be in danger of losing his vocation, but that otherwise God would provide. Allen had already founded a missionary house at Douai in 1568, and its success may be estimated from the fact that one hundred and sixty priests, most of them from the secular clergy, who had been trained there, were martyred for the Faith. He had succeeded also in obtaining another establishment in Rome. In 1578, however, when the occupants of Douai were expelled, they were lodged at Rheims in the house of the Jesuits. Meantime, the Roman foundation had been entrusted to the Society; and with these two sources of supplies now at his disposal, Father Mercurian determined to begin the great work.