After being released from prison, he lived and worked from the house of Mrs. Meany in Westminster, England in secret.
In 1601 a government spy described Blackwell as "about 50 years of age, his head brownish, his beard more black, cut after the fashion of a spade, of stature indifferent, and somewhat thick, decently attired"[2] 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.
His instructions enjoined him to work in close consultation with the head of the Jesuit mission in England.
According to John Hungerford Pollen, Blackwell's "main defect appears to have been an entire want of experience in government, Joined wit xaggerated ideas of his position as Superior.
"[4] The English government was keen to turn the controversy to its advantage, and encouraged Blackwell's "Appellant" enemies behind the scenes.
The upshot of the third and final appeal was that Blackwell's powers were confirmed, but he was censured for his lack of tact[3] and ordered in future not to communicate to the Jesuits any matters pertaining solely to the mission of the secular clergy.