During this period as a clandestine missionary in England, Allen formed the conviction that the people were not set against Rome by choice, but by force and by circumstances; and the majority were only too ready, in response to his sermons and ministrations, to return to Roman Catholicism. He was convinced that the Protestant hold over the Kingdom, favoured by the policies of Elizabeth, could only be temporary. When his presence was discovered by the Queen's agents, he fled from Lancashire and withdrew to Oxford, where he had many acquaintances.