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Allen caused the government, even after the rising in the north was suppressed; and secondly in the almost universal support which was given to the seminary system by the catholics in that district. Strype informs us that in 1567 ‘religion, in Lancashire and the parts thereabouts, went backwards, papists about this time showing themselves to be numerous, mass commonly said, priests harboured, the Book of Common Prayer and the church established by law laid aside, many churches shut up and cures unsupplied, unless with such popish priests as had been ejected.’

Allen's open hostility to the established church greatly alarmed the magistrates of Lancashire, but he eluded their search for him, and retired to the neighbourhood of Oxford, where he continued the same agressive tactics, and composed two controversial treatises on the priesthood and on indulgences. Once more obliged to seek a new place of refuge, he found a shelter in the county of Norfolk, in the family of the Duke of Norfolk, who, though himself a protestant, gave protection to several learned catholics. It was while living here that he wrote ‘Certain Brief Reasons concerning Catholic Faith.’ Afterwards he revisited Oxford and converted an old acquaintance, whose parents pursued Allen so closely that he was forced to leave England after he had resided here about three years. He finally landed, in 1565, in the Low Countries, and never returned to England.

After being ordained priest at Mechlin, where he had previously received all the other orders, he read lectures on theology in the splendid college which the Benedictine monks possessed in that city. In the autumn of 1567 he set out on a pilgrimage to Rome in the company of his old master, Morgan Philipps, and of Dr. Vendeville, at that time professor of canon law in the university of Douay, and afterwards bishop of Tournay. The object of Dr. Vendeville's journey was to lay before Pope Pius V a project which he had formed for the conversion of the infidels, or, according to another account, for the relief of slaves out of Barbary (, Church History, ii. 45). He spent the whole winter in Rome, but to no purpose, for the sovereign pontiff was too much occupied with other more weighty matters to attend to him. In the spring he returned with Allen to the Netherlands in a somewhat despondent state of mind, and on the journey disclosed to his companion the subject of his grief. Allen at once seized the opportunity of giving Dr. Vendeville's zeal a new direction. He pointed out the great needs of the catholics in the Netherlands and England, and showed him how much easier than to carry out his other plan it would be to succour them. He dwelt particularly on the danger which threatened the church in England through the dying out of the ancient priests, and suggested, as a remedy for the evil, the foundation of a college for English students abroad. Writing some years later to Dr. Vendeville, he thus reminded him of what they had agreed upon in the course of this conversation, which resulted in the establishment of the English college at Douay, and, by degrees, of all the other colleges and religious communities on the Continent that subsequently furnished England with missionary priests. ‘Our first purpose was to establish a college in which our countrymen, who were scattered abroad in different places, might live and study together more profitably than apart. Our next intention was to secure for the college an unbroken and enduring existence by means of a constant succession of students coming and leaving; for we feared that if the schism should last much longer, owing to the death of the few who, at its beginning, had been cast out of the English universities for the faith, no seed would be left hereafter for the restoration of religion, and that heresy would thus obtain a perpetual and peaceful possession of the realm, there being no one to make reclamation, even though an opportunity should offer at the death of the queen or otherwise’ (Records of the English Catholics, ii. 54). Such was Allen's aim in the establishment of a college: first to enable English students abroad to have the benefit of collegiate training; secondly, to form a body of learned priests capable of restoring the catholic religion in England whenever circumstances should permit; thirdly, to instruct in their religion English youths who might come for their education to the college. The missionary work in England was an after-thought.

Allen at once began to put into execution the plan he had formed for the establishment of a college in the university of Douay. On Michaelmas day 1568, with the approbation of Dr. Matthew Galen, chancellor of the university, and Dr. Vendeville, both of whom warmly supported his project, he took possession of a large house, which he had hired near the theological schools, and began to live there in collegiate form with a few students, English and Belgian. Among those who began the work with Allen were Morgan Philipps, Richard Bristow, John Marshall, Edward Risdon, and John White. They were afterwards joined by Dr. Stapleton, Dr. Bailey, Dr. Webb, and other eminent divines, most