He went in 1547 to Oriel College, Oxford, and in 1556 became principal of St Mary Hall and proctor. According to Anthony Wood, he was appointed to a canonry at York in or about 1558; he therefore had already entered the clerical state by receiving the tonsure. On the accession of Elizabeth I, he was deprived upon refusing the Oath of Supremacy, but remained in the university until 1561. His known opposition to the new learning in religion giving much offence, he escaped from England and went to Louvain, where were gathered many students who had left the English universities for conscience' sake. Here he continued his theological studies and began to write controversial treatises. In 1562, on account of health, he returned secretly to Lancashire and did much, by exhortation and private meetings, to restrain those Catholics who attended the new services in order to save their property from confiscation. His presence being known to the government, he left Lancashire and retired to the neighbourhood of Oxford, which he frequently visited, and where he influenced many of the students. After writing a treatise in defence of the priestly power to remit sins, he was obliged to leave and retired to Norfolk, leaving England soon after in 1565. He returned to Flanders, was ordained at Malines, and began to lecture in theology at the Benedictine college in that city. In 1567 he went to Rome for the first time, and there began his plan for establishing a college where English students could live together and finish their theological course. The idea subsequently developed into the establishing of a missionary college, or seminary, to keep up a supply of priests for England as long as the country remained separated from the Holy See. With the help of friends, and notably of the Benedictine abbots of the neighbouring monasteries, a college was established at Douai (September 29, 1568); and here Allen was joined by many of the English exiles. This college, the first of the seminaries ordered by the Council of Trent, received the papal approval shortly after its establishment; the king of Spain took it under his protection and assigned it an annual grant. Allen continued his own theological studies and, after taking his doctorate, became regius professor at the university. Pope Gregory XIII in 1575 granted him a monthly pension of 100 golden crowns, and, as the number of students had now risen to one hundred and twenty, summoned him to Rome to undertake the establishing of a similar college in the papal city.
By Allen's advice, the old English hospice was turned into a seminary and Jesuits were placed there to help Dr Maurice Clennock, the rector. The pope appointed Allen to a canonry in Courtrai and sent him back to Douai (July 1576); but here he had to face a new difficulty. Besides the reported plots to assassinate him by agents of the English government, the insurgents against Spain, urged on by Elizabeth's emissaries, expelled the students from Douai as being partisans of the enemy (March 1578). Allen moved his establishment to Reims under the rotection of the house of Guise; and it was here that the English translation of the Scriptures, known as the Douai Version, was begun under his direction.
In 1577 he began a correspondence with Robert Parsons, the Jesuit, an intimacy that was fraught with disaster. He was summoned again to Rome in 1579 to quell the first of the many disturbances that befell the English college under the Jesuit influence. Brought now into personal contact with Parsons, Allen fell completely under the dominating personality of the redoubtable Jesuit, and gave himself up entirely to his influence. He arranged that the Society should take over the English college at Rome and should begin the Jesuit mission to England in 1580. This short-sighted policy was the cause of much grave trouble in the near future. Returning to Reims he began to take a part in all the political intrigues which Parsons' fertile brain had hatched for the promotion of the Spanish interest in England. Allen's political career dates from this period. Parsons had already intended to remove Allen from the seminary at Reims, and for this purpose, as far back as the 6th of April 1581, had recommended him to Philip II. to be promoted to the cardinalate. In furtherance of the intrigues, Allen and Parsons went to Rome again in 1585 and there Allen was kept for the rest of his life. In 1587, during the time that he was being skilfully played with by Philip's agents, he wrote, helped by Parsons, a shameless defence of a shameful deed. Sir William Stanley, an English officer, had surrendered Deventer to the Spaniards; and Allen wrote a book in defence of Stanley, saying that all Englishmen were bound, under pain of damnation, to follow the traitorous example, as Elizabeth was no lawful queen. He shared in all the projects for the invasion of England, and was to have been archbishop of Canterbury and lord chancellor had they succeeded. Representing in reality only his own party, Allen had on the continent the position of the head of the Roman Catholics of England; and as such, just after the death of Mary, Queen of Scots, he wrote to Philip II (March 19, 1587) to exhort him to undertake the enterprise against England, and declared that the Catholics there were clamouring for the king to come and punish "this woman, hated by God and man."
After much negotiation, he was made cardinal by Pope Sixtus V on the 7th of August 1587, nominally to supply the loss of the queen of Scotland, but in reality to ensure the success of the Armada. On his promotion Allen wrote to Reims that he owed the hat, under God, to Parsons. One of his first acts was to issue, under his own name, two violent works for the purpose of inciting the Catholics of England to rise against Elizabeth: "The Declaration of the Sentence of Sixtus V." a broadside, and a book, ''An Admonition to the nobility and people of England'' (Antwerp, 1588). On the failure of the Armada, Philip, to get rid of the burthen of supporting Allen as a cardinal, nominated him to the archbishopric of Malines, but the canonical appointment was never made. Pope Gregory XIV made him librarian at the Vatican; and he served on the commission for the editing of the text of the Vulgate. He took part in four conclaves, but never had any real influence after the failure of the Armada.
Before his death, which took place in Rome on the 16th of October 1594, he found reasons to change his mind concerning the wisdom of the Jesuit politics in Rome and England, and would have tried to curb their activities, had he been spared. The rift became so great that ten years after his death, Agazzari could write to Parsons: "So long as Allen walked in this matter (the scheme for England) in union with and fidelity to the Company, as he used to do, God preserved him, prospered and exalted him; but when he began to leave this path, in a manner, the threads of his plans and life were cut short together." As a cardinal Allen had lived in poverty and he died in debt.
While we cannot withhold a tribute of respect from Allen for his zeal and earnestness, and recognize that his foundation at Douai survives to-day in the two Catholic colleges at Ushaw and Ware, it is impossible to deny that he injured the work with which his name will ever be associated, by his disastrous intercourse with Father Parsons. Known as a sharer in that plotter's schemes, he gave a reasonable pretext to Elizabeth's government for regarding the seminaries as hotbeds of sedition. That they were not so is abundantly proved. The superiors kept their political actions secret from the students, and would not allow such matters even to be talked about or treated as theoretical abstractions in the schools. Dr Barrett, writing (April 14, 1583) to Parsons, makes open complaint of Allen's secrecy and refusal to communicate. How far Allen was really admitted to the full confidence of Parsons is a question; and his later attitude to the Society goes to prove that he at last realized that he had been tricked. Like James II. with Fr. Petre, Allen had been "bewitched" for a time and only recovered himself when too late.
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