O'Roghan alleged that he had been tortured by members of this commission, and Fitzwilliam was instantly directed on strict instruction from the Queen to resume his original investigation and forward the findings to the Privy Council in London. Perrot faced a moment of crisis when further allegations were made – most notably by his former secretary, Henry Bird – of his frequent use in private conversation of violent language against the Queen. He was also accused of having prior knowledge of the rebellion in 1589 of Sir Brian O'Rourke (later extradited from Scotland and hanged at London), which had occurred under the government of Bingham in Connaught.