After the death of Cardinal Allen in 1594, the leadership of the clandestine Catholic Mission in England was thrown into disarray. On 7 March 1598, Pope Clement VIII appointed Blackwell archpriest over the secular clergy in England. Six assistants were named for him and another six were left to his discretion. As Archpriest, he lodged at the town house of Anthony-Maria Browne, 2nd Viscount Montagu, when in London. His instructions enjoined him to work in close consultation with the head of the Jesuit mission in England.