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In 1575 Allen made a second journey to Rome, where he helped Pope Gregory XIII to found another college For this purpose possession was obtained of the ancient English hospice in Rome, now turned into a seminary to send missionaries to England and Jesuits were placed there to help Dr Maurice Clennock, the rector.
Allen wrote that all Englishmen were bound, under pain of damnation, to follow this example, as Elizabeth was no lawful queen.
Allen helped plan the invasion of England, and was to have been Archbishop of Canterbury and Lord Chancellor had it succeeded.
He was the third son of John Allen of Rossall, Lancashire, and at the age of fifteen went to Oriel College, Oxford, where he graduated B. in 1550, and was elected Fellow of his College.
On the accession of Elizabeth, and the re-establishment of Protestantism, Allen was one of those who remained most stanch on the Catholic side, and it is chiefly due to his labours that the Catholic religion was not entirely stamped out in England.
The means of support included, besides Allen's private income, and other voluntary donations, a yearly pension of 200 ducats from the King of Spain, and later on one of 100 gold crowns a month from the Pope.